Currently included settings:

•  Experience
•  Damage
•  Heal Duration
•  Legendary Spawn Chance
•  Sneak Attack Damage
•  Stealth
•  AI
•  Sprint Cost
•  Limbs
•  Loot Tweaks
•  Barter Tweaks
•  Carry Weight
•  Fusion Core Drain
•  Lockpicking
•  Health
•  Radiation
•  Fall Damage
•  Stimpack Speed
•  Food Healing
•  Respawn Rates
  

Nexus Mod Manager: A functional FOMOD installer is included which will allow you to select either a prebuilt balance patch, or pick custom .esps with the values you're looking for.

Manual: Browse through the categories for descriptions of the files and suggested settings for any modifications you wish to use.  Use no more than one file per subcategory (01A, 01B, etc.)


Rebalancer is a fairly large mod, so there's bound to be some compatibility issues with other gameplay mods.  Luckily, Rebalancer's modularity allows you to pick and choose what  parts to use, so you're free to mix in other gameplay mods.

General rule of thumb: if you think they edit the same thing, they probably do.
The only oddball modules that have extra edits to make sure things work properly are radiation and quicker stims, which both edit the medic perk.

You may also be interested in Personal Patch Emporium by lunarionsilver which includes a handful of patches for Rebalancer and other mods.

Experience

 01A - XP Mult
       - Modifies global experience modifier, and will affect any other experience changes.
       - Format: Percent of base experience
       - Suggested: 50.

 01B - Exploration
       - Modifies (or removes) experience gained from hacking, lockpicking, persuasion, and discovering locations.
       - Format: Percent of base experience
       - Suggested: 200

 01C - Crafting
       - Modifies (Or removes) experience gained from modifying armor and weapons, as well as cooking and using the chem station
       - Format: Percent of base experience
       - Suggested: None, use default experience.

 01D - Settlement
       - Modifies (Or removes) experience gained from settlement building.
       - Format: Percent of base experience
       - Suggested: 50

Combat

02A - Player Damage
       - Changes damage done by player on all difficulties.
       - Format: Percent of base damage
       - Suggested: 150

 02B - NPC Damage
       - Changes damage done by NPCs on all difficulties.
       - Format: Percent of base damage
       - Suggested: 200
 
 02C - Chem Duration
       - Modifies the amount of time required for healing effects to occur on all difficulties.
       - Format: Percent of default time.
       - Suggested: 750%

 02D - Legendary Chance
      - Modifies (Or removes) the chance of legendary spawns, relative to normal (100). Default survival mode is 300.
      - Format: Percent of normal mode.
      - Suggested: 200

 02E - Sneak Attack Damage
      - Modifies (Or removes) the damage bonus multiplier of sneak attacks.
      - Format: Percent of base bonus
      - Suggested: 50

 02F - Stealth
      - Rebalance of stealth.  Increased effect of light on stealth, reduced penalties for movement sound.  Interior sneak range decreased slightly in light/medium. Outdoor range increased by ~50% in all modes.  Various other tweaks to make stealth more intuitive and rewarding to properly built characters.
      - Suggested: Light

 02G - AI Tweaks
      - Rebalance of AI. NPCs will be more aggressive in packs, with increased chances of flanking.  
      - Light is minor changes compared to vanilla, with heavy being rather noticeable.
      - Suggested: Light

 02H - Sprint Cost
      - Modifies (Or removes) the action point cost of sprinting.
      - Format: Percent of base cost
      - Suggested: 125

 02I - Crippled Tweaks
      - Numerous changes to limbs: all versions add more variance to localized damage.  Damage to limbs, and protection offered by armor both increased, heaviest in heavy.  Medium and heavy feature more penalties for crippled limbs.
      - Suggested: Light

 02J - Limb Regen
       - Increases the delay before automatic limb regen takes effect.  Disabled will not remove limb regen, but will drastically increase time before regen happens, effectively disabling it.
       - Format: Percent of default time.
       - Suggested: 150

Loot

 03A - Less Ammo
       - Reduces the amount of ammo found.
       - Format: Percent reduction
       - Suggested: 50

 03B - Less Chems
       - Slightly reduces (~25%) the amount of chems found in loot.  Less Chems+ greatly (>75%) reduces the amount of chems found in loot.
       - Suggested: Yes

 03C - Less Caps
       - Slightly reduces (~25%) the amount of caps found in loot and rewarded.  Less Caps+ reduces this further (~50%).
       - Suggested: Yes

 03D - Barter
       - Changes the default buy and sell prices so merchants offer less and charge more, while keeping charisma and perks lucrative.
       - Light has the lowest effect, while heavy has the highest.
       - Suggested: Light

 03E - Weighted Misc
       - Adds weight to various weightless junk and misc items.
       - Suggested: Yes

 03F - Heavier Ingestibles
       - Doubles the weight of chems.
       - Suggested: Yes

 03G - Base Weight
       - Modifies base carry weight.  
       **Carry weight may not update until your strength has changed (using chems/alcohol, or strength modifying equipment will work).
       - Format: Carry weight
       - Default: 200
       - Suggested: 100

 03H - Weight Per Strength
       - Modifies the amount of carry weight added per point of strength
      **Carry weight may not update until your strength has changed (using chems/alcohol, or strength modifying equipment will work).
       - Format: Carry weight/strength.
       - Default: 10
       - Suggested: 15

Fusion Core Drain

 04A - Fusion Core Movement Drain
       - Modifies (or removes) the amount of fusion core drain caused by running in power armor.
       - Format: Percent of base drain
       - Suggested: 75

 04B - Fusion Core AP Drain
       - Modifies (or removes) the amount of fusion core drain caused by action point use (including sprinting).
       - Format: Percent of base drain
       - Suggested: 75

 04C - Fusion Core Jetpack Drain
       - Modifies (or removes) the amount of fusion core drain caused by using a jetpack.
       - Format: Percent of base drain
       - Suggested: 125

 04D - Fusion Core Jump Drain
       - Adds fusion core drain to jumping in power armor.
       - Format: Fusion core drain per jump
       - Suggested: .25

Lockpicking

 05A - Difficulty Scale
       - Modifies the differences in difficulty between lockpick grades.
       - Positive files increase difficulty, negative files reduce difficulty
       - Format: Percent of difficulty change.
       - Suggested: +25
 
 05B - Sweet Spot Size
       - Modifies the size of sweet spots for all lock difficulties
       - Format: Percent of sweet spot size
       - Suggested: No

 05C - Partial Size
       - Modifies the size of partial pick spots for all lock difficulties
       - Format: Percent of partial size
       - Suggested: 75

 05D - Break Chance
       - Increases the chance of lockpicks breaking.
       - Break Chance Scaled makes harder locks do more damage to lockpicks.
       - Format: Percent change
       - Suggested: Scaled - 100

 05E - Locksmith Bonus
       - Changes the bonus provided per level of locksmith from sweetspot starting location to sweetspot size.
       - Suggested: yes

Health
 06A - Endurance Bonus
       - Modifies the flat HP bonus provided by endurance.
       **Endurance or level must be modified to take effect (chems, armor etc will work).
       - Format: Bonus
       - Default: 5
       - Suggested: 7

 06B - Endurance Level Bonus
       - Modifies the per level HP bonus provided by endurance.
       **Endurance or level must be modified to take effect (chems, armor etc will work).
       - Format: Percent of default bonus (0.5)
       - Suggested: 125

 06C - Level Bonus
       - Modifies the base (non endurance) level bonus provided to HP.
       **Endurance or level must be modified to take effect (chems, armor etc will work).
       - Format: Bonus
       - Default: 2.5
       - Suggested: 1.5

 06D - NPC Level Bonus
       - Modifies the base level bonus provided to HP for NPCs.  May not apply to already spawned NPCs.
       - Format: Bonus
       - Default: 5
       - Suggested: 7

 06E - Radiation
       - Modifies the health penalty from radiation, and the strength of rad away.  May alter maximum amount of rads that can be taken.
       - Format: Percent of change.
       - Suggested: 150

 06F - Fall Damage
       - Rebalances fall height.  Damage will start applying from lower heights, but match vanilla around a four story fall.
       - Fall Damage 50 will also half fall damage, 150 and 200 will increase it.
       - Format: Percent of damage (compared to Fall Damage - 100)
       - Suggested: 100

 06G - Leg Damage
       - Increases damage done to legs by falling.  Based on health, so changing fall damage will also have an effect.
       - Format: Percent of default leg damage.
       - Suggested: 150

 06H - Quicker Stims
      - Decreases the time stimpaks take to apply their effect, but stimpaks now have weight.
      - Format: Percent Reduction
      - Suggested: 40

 06I - Food Healing
       - Reduces the healing effect of food.  Currently only available at 50%, chance of low compatibility with other mods.
       - Format: percent of default healing
       - Suggested: No

Misc

 10A - General Respawn
       - Changes the time for exteriors and some interior cells to respawn.
       - Format: Days
       - Default: 7
       - Suggested: 10

 10B - Dungeon Respawn
       - Changes the time for cleared cells to respawn.
       - Format: Days
       - Default: 20
       - Suggested: 20 (No .esp)

 10C - Vendor Respawn
       - Changes the time for vendors to restock.
       - Format: Days
       - Default: 2
       - Suggested: 5

Experimental

 **Features not included in main package to due to known or unknown bugs.  Modules will be included properly when FO4Edit allows the records to be edited safely.

 11A - Companion Weight
       - Removes the penalties to companion carry weight for human NPCs, reduces it for non-human NPCs.  
      **KNOWN EFFECT: causes human companions to lose their custom textures.
      **Companion carry weight may not update automatically.  Equipping them with gear that modifies strength, or manually changing their strength via console will fix this.
       - Suggested: No (unless you don't care about companions losing their custom textures)

 11B - SPECIAL Perks
       - Higher levels of perks will require higher levels of the appropriate attribute, but a lower level requirement (generally 3 levels per point).
       - Perk chart will show coloured icons even if you can't meet the attribute requirements, but no other known side effects.
       - Suggested: If you'd like a more specialised low level character.



 - Version 1.036 - 01.03.16
   - Existing Modules:
     - Less Ammo updated to include changes to scrounger
     - SPECIAL Perks updated with perk fixes

 - Version 1.035 - 24.01.16
   - Existing Modules:
     - NPC Carry weight and SPECIAL Perks updated for beta patch.

   - Moved prebuilt settings into main archive.

 - Version 1.034 - 04.01.16
   - Existing Modules:
     - Vendor lists altered in less ammo and less caps, to counteract the reduction in vendor ammo and bobbypins caused by the modules.

   - New Module:
     - SPECIAL Perks.  Because there hasn't been anything new since 1.03.

- Version 1.033 - 22.12.15
   - Existing Modules:
     - Redid Break Chance Scaled modules.  About half as severe as they were previously.
     - Increased bobbypin count in less caps/+ slightly (still less than vanilla in both modules)
     - Changed Ninja perk descriptions to reflect changes in Sneak Attack Damage modules
     - Increased amount of time NPCs care about dead bodies in stealth overhaul.
     - Few more tweaks to AI.  They should care slightly more about their own life now.

 - Version 1.032 - 13.12.15
   - Updated 06I - Food Healing with newer version of FO4Edit.

 - Version 1.03 - 12.12.15
   - New Modules:
     - Endurance Level Bonus: affects the HP bonus per point of endurance per level.
     - Respawn times
     - Vendor restock times
     - Chem Duration: Same thing as choosing survival, but configurable.

   - Existing Modules:
     - Localization and crippled merged into single module: limb tweaks.
     - Stealth, Combat and Limbs moved out of beta and included with prebuilt .esps.
     - Survival Player and NPC Damage changed to Player and NPC damage.  Now affect all difficulties.
     - Survival Heal Strength removed.  Replaced with chem duration.
     - Sneak attack damage now includes grenades.
     - Radiation module remade using a different setting. Radaway rebalanced accordingly, and affected properly by medic perk.
     - Quicker stims now works properly with medic perk.  
     - Renumbered many health modules to fit endurance level bonus in a logical place
     - Added player damage 25.
     - Added some missing chems to heavier chems
     - Fixed some fomod typos, and rearranged a number of modules.

 - Version 1.025 - 06.12.15
   - New Modules:
     - Added module to remove the carry weight penalty for human companions, reduced for non-human
     - Added new beta module for damage localization

   - Existing Modules:
     - Further tweaks to AI beta, added heavy option.
     - Further refined stealth tweaks, increased importance of armor weight.  Added medium and heavy options (previous version was ~light)
     - Added dirty and purified water to food healing at 75%
     - Increased values for all versions of barter, light is roughly what medium was, medium heavy, and heavy a step past what it used to be.
     - Added module to "disable" limb regen.  Regen will still occur at some point, it'll just be in a really long time.

 - Version 1.02 - 30.11.15
   - New Health modules: Endurance Bonus, Level Bonus, NPC Level Bonus, Fall damage, Leg Damage, Limb Regen, Food Healing
   - Heavier Ingestibles renamed to heavier chems, food entries and rad-away removed for compatibility
   - Small tweaks to less caps/+, less chems/+
   - Two new options for global experience: 15%, 35%
   - New beta module for crippled effects.
   - Further refinement of Stealth Tweaks
   - Added another option for AI tweaks.  Still beta, previous version renamed to light.
   - Minor fomod tweaks
   - Small changes to prebuilt options
   - included settings used for prebuilt files

 - Version 1.01 - 26.11.15
   - Small tweaks to less ammo 25, 50, less caps, less chems
   - Added less ammo 75
   - Added less chems+
   - Added less caps+
   - Added legendary chance 500, 600
   - Added 4x survival damage for players and NPCs
   - Added Quicker Stims
   - Added Stealth Tweaks Beta
   - Added AI Tweaks Beta
   - Stimpak weight removed from misc weight and heavier chems for compatibility reason.  Added as part of quicker stims.
   - Fix to sneak attack .esps not applying to some melee weapons
   - Increased number of premade .esps to three.

 - Version 1.0 - 24.11.15
   - Initial Release