The following rules variants are currently in use; this is just a place to summarize and refresh memories on the subject. Some of these variants are borrowed from official books, and others are tweaked and customized to fit the campaign.
All major PCs and NPCs are considered gestalt characters - they take two character classes at each level, and receive the best of both classes (skill points and HP increases use the best of both; feats and abilities earned stack.)
Characters gain a bonus to their armor class based on their current level and character class. (Monsters that have no class levels but can equip armor also receive a bonus.)
Armor provides a lower bonus to armor class, but also provides damage reduction, making better armor resistant to damage. In short, divide normal AC by 2 and round down for DR provided, and subtract this from AC to determine new AC. For natural armor, divide natural armor bonus by 5 and round down to determine DR, and subtract that from monster AC to determine new monster AC.
Each character has reserve hit points that, when not in combat, 'flow' into normal hit points, replenishing them and thus giving people a chance to get back up to full fighting strength quickly. Reserve hit points become normal hit points at the rate of one point per minute. Reserve hit points are recovered only after all normal hit points are recovered, and can be recovered in ways similar to normal hit points.
Whenever a character takes more than Con + (Hit Dice or Levels x 2) damage in one shot, they must make a Fortitude save vs DC 15 or immediately be reduced to dying (-1 HP) regardless of their current hit points).
Creatures and characters are considered dead when they reach negative hit points equal to half their normal hit point total, either through injury or bleeding. Any attack that kills a character outright reduces them to this point automatically.
If you take more than half your current hit points in damage from a single attack, you are clobbered; you can only take a standard action (such as a single attack). After that turn, you are no longer clobbered (and can act normally.)
All rolls that land within the critical threat range count as critical hits if they strike; a 20 is always an automatic hit, and a 1 is always an automatic miss.
A called shot or damage to a specific part of the body causes a -2 to anything involving that body part if it is successfully damaged. A character can make a Fortitude save at (DC 10 + damage) to resist this effect and 'tough it out'; otherwise, the effect will be removed when the wound is healed.
Damage affects Climb, Craft, Disable Device, Escape Artist, Forgery, Heal, Open Lock, Sleight of Hand, and Use Rope checks, as well as attack rolls.
Damage affects Climb and Swim checks; attack rolls; and Strength checks.
Damage affects Appraise, Craft, Decipher Script, Disable Device, Forgery, Open Lock, Search, Sense Motive, Spellcraft, and Spot checks; Survival checks (for tracking); initiative checks; Dexterity checks; ranged attack rolls; Reflex saving throws.
Severe damage to both eyes causes a character to become blinded.
Damage affects Listen checks; initiative checks.
Severe damage to both ears causes a character to become deafened.
Damage affects Balance, Climb, Jump, Move Silently, Ride, Swim, and Tumble checks; Reflex saving throws; and Dexterity checks.
Like psions, magical classes have spell points that they use to cast spells, instead of having specific spell limits. Wizards still have to study spellbooks in order to learn new spells, and sorcerers are still limited to only using the spells they have developed. Spell points are recovered when the person receives a full eight hours of rest, regardless of how much sleep they require normally. Spells cast by more skilled casters are more powerful for the same energy cost. Certain special items may restore spell points, or transfer spell points to others at an imperfect rate.
Spells can be 'charged' – using extra spell points and time to increase the effective level of the caster up to the maximum for the spell. Each extra caster level costs 1 extra SP and adds 1 round to the casting time if the spell takes less than one round to cast normally, or costs 2 SP and increases casting time by 100% otherwise.
Spellcasters automatically become fatigued when their spell points are reduced to less than half full, and exhausted when reduced to less than 1/4; if fatigued by other means, their spell points immediately drop to 1/2 of maximum if currently higher, and if exhausted, they immediately drop to 1/4 of maximum if currently higher.
One full hour of rest restores an 'exhausted' character up to 'fatigued' and restores spell points up to 1/3 of max; two hours of rest restore spell points up to 2/3 of max, and a full eight hours of rest is required to restore spell points to maximum.
(per DMG, p300-301)
Fatigued characters suffer a -2 to Strength and Dexterity and cannot run or charge until they have received eight full hours of rest.
Exhausted characters suffer a -6 to Strength and Dexterity and can only move at half speed.
Metamagic feats and powers increase the spell point cost of spells according to the new level of the spell thus altered (an empowered first-level spell would cost 5 SP to cast, as if it were a 3rd-level spell).
Characters can push themselves beyond the listed spell point limits, but must succeed on a Concentration check (DC 20 + spell level). Failing this check inflicts lethal and nonlethal damage on the caster equal to the level of the spell cast. Add a cumulative -2 every time this is used until the caster gets some rest.
Psions, rangers, sorcerers, bards, and similar 'spontaneous casters' have a specified range of powers or spells that they can access. They can change these powers by taking time to study, similarly to how wizards transcribe spells into spellbooks (see below).
Clerics, paladins, and other divinities are gifted their powers by their gods; they can choose any power their god has granted access to (and likewise, cannot use spells their god denies them.)
Wizards and other 'study casters' have a specific spell list that they must use, but can easily change it through study. A wizard can change their current spell list if they are fully rested and have at least fifteen minutes (to swap in a single spell) to one hour (if major changes need to be made) to study.
Deciphering an new and unfamiliar magical writing (such as in a found spellbook or scroll) requires a Spellcraft (or Psicraft, for psions) check at DC 20 + the spell's level. If it fails, the character cannot attempt to read it again until the next day. Success is automatic if the original writer is available to assist or if a read magic or similar spell is cast. Deciphering a magical writing allows the reader to identify it and give some idea of its effects (allowing them to use it, if it's a scroll, or study it, if it's a spell.)
Using a borrowed spellbook to study a spell requires a Spellcraft check at DC 15 + spell level (after it has been deciphered).
Transcribing a spell into your spellbook requires a day's study, plus a Spellcraft check at DC 15 + spell level; failure means you cannot try again until you gain another level in Spellcraft.