Hmm, hard to narrow it down.
Let's see, 5 rules eh? (Yeah yeah people are adding more but I don't want to write a 10,000 line post).
1. TIMING MODEL GETS TOSSED! I replaced this with my own system (it's a long document I'm constantly revising). I don't want to have to deal with spending 20 minutes figuring out "ok, so was that a partial action? Then a move action. What was a standard action again? Ok so then does this count as my free action from this feat?" That's gone. I use a serial (things happen one after another, this IS turn based combat afterall) model where a round is 6 seconds, and anything that makes a physical change takes at least 1 second. Including "free" actions. Free actions and 5' steps are 1, partial and move are 2, hustle is 3, standard is 4, full attack is 5, and full round is 6. Haste and Slow are precisely defined (makes your round 8 sec or 2 sec) and so is just about every possible thing a character can do, by categories and how many seconds each type takes. I.e. "If I'm hasted, can I cast 2 spells per round?" "Yes but not 2 and move." or "Can I run over, chop this guy, then supreme cleave through these 40 people, then jump across this chasm so they can't get me?" "Not likely. What's your base move again?" etc.
2. Rebuilt spell system. I.e. spell points, exponential costs per spell level (0=1, 9th = 512), ability mod x level points added per caster level (an average 20th lvl wizard has about 1050), sorcerers get x1.5. Wizards don't "lose" spells when cast, but they can only "memorize" a few at a time (max ability mod, with a progression table), and have to spend 8 hours to change them. Sorcerers can cast anything they know at any time (provided they have points), and know max ability mod of each level, with a progression table. Clerics still use spell-level system but dynamic cast ANY spell on their list as a "miracle" from their deity. Great when the unexpected happens.
3. Rebuilt melee system. No damage rolls, damage is based on attack roll exceeding AC x weapon multiplier (1d6 = 1.0, others are calculated from avg dmg vs 3.5 on 1d6) + modifiers (like STR). Power attack gets removed since it's automatic with this. I use it because it prevents "I chop you with my power attacking +5 holy flaming longsword for 47 points of damage!" vs "Umm my 20th level fighter hits you with his mighty bow... for umm... 1d8... add strength... 6 points of damage!" Sorry, high level bowman WILL take your head off in one hit! Threats mean if you hit, roll again as many times as you have critical multiplier > 1 and add the results of any hits you get. People with crap AC (i.e. spellcasters) tend to die very fast vs high level fighters, but then they can cast fireball and such alot more in my world, so they just try to stay at range. High level fighter type vs fighter type with good AC tends to take forever for one to beat the other down (they average alot less damage than in a lopsided fight). Makes for good climactic boss battles.
4. Karma stat. I like to reward roleplaying xp and creative ideas with points. Everyone starts with 10 (Average). The ability modifier generated by this stat modifies any luck rolls I ask you to make. Points are redeemable for 10% of the XP you need for your next level (yes you can spend it on items too) or 10% of the starting PC gold of someone of your level as listed in the DMG or equipment worth that much. 10 buy a 1 point stat increase, 15 buy a feat. People who buy advantages are thus less lucky because they should be able to get by with their advantages.
5. Totally reworked classes in some cases. Ex ranger: Gets all sorts of nifty new stuff, favored enemies are TYPES, i.e. abberations, magical beasts, humanoids. Stackable threat range increase (expert critical) vs favored enemies. Ambush feat lets you make hide checks to surprise people (surprise rounds are good). Gains bonuses in more terrain types at higher levels. Another EX: Paladin. Not a prestiege class but dumps the worthless spells, remove disease, and turn attempts. Gets permanent supernatural auras, prot from evil 5th, magic circle 10th, holy aura 15th, greater aspect of the deity (half celestial template) at 20th. Smiting reworked, gets 1 at 1st + 1 more smite every 3 levels. Smite = make a touch attack, if you miss or the opponent is non-evil it's wasted. Success means they make a fort save DC 10 + 1/2 your paladin lvl + your charisma modifier OR BE DISINTEGRATED (and lobbeth thy holy hand grenade towards thy foe, and he, being naughty in my sight, shall snuffeth). No dmg if they succeed, you can smite only once per round as a standard action. Things with no con modifier (like undead) still fort save (boy are they in trouble). Bards get 6 skill points/lvl, and uncanny dodge instead of evasion. Barbarians get evasion instead of uncanny dodge and some better feats (like improved critical) as they go. Monks are pretty good as is but get fighter base attack increase (they fight all the time, DUH!). Rogues get to trade in 10 skill points for a feat at their option. Druids... not done fixing that yet.