Classes: Add Swashbuckler and some sort of Noble pc class. Explain the Paladin ethos a LOT more (maybe that will finally kill the "Can a Paladin do X?" disputes).
Let Rangers gain abilities with Double-Weapons. [Edit: This was done already for 3.5, so pardon my edition fugue]

Replace Sorceror with a spell-point character with its own spell-list stolen from the Psion list and renamed (psionic serial numbers filed off). Call it "Sorceror" so no one gets upset.

Races: Make the half-elf less teh suk, or just remove them. Make the dwarf less uber. Give half-orcs something interesting. (Orcish double-ax familiarity would be nice, as would be scent)
Feats: Put in 2 more weapon focus/spec. feats for the fighter at 16th and 20th prereqs., to bump up to +3 TH, +6 DA. Replace Toughness with Improved Toughness. Allow Saving Throw feats to be taken multiple times and stack. Allow Rapid Reload to be taken with slings, and also to be taken multiple times with Heavy Crossbow to stack. Put in feats to let Sneak Attack apply to more critters.
Combat: Take out the "stand up provokes Aoo" rule.
Spells: BEEF up the combat spells so that mages can actually do real damage to foes (who if no one has noticed have gained more hit points since 2nd edition!), put them to sleep, hold them for more than a round, etc.
Skills: give everyone one max'd out skill in one Craft, Profession or Perform. as their background skill. Reduce number of skills (Spot/Listen/"scenting" can all become "alertness", for instance).
Spells: Once and for all, for the love of god and all that is holy, definitively explain what polymorph, shape change, alter self, druid wild shape, etc., can and cannot do.
Put in guidelines on Summon X spells to expand the lists.
Make illusion magic more attractive as an option. Maybe rethink the whole way it is done.
Alignment: Maybe give some examples of what fits in what category (Ignoring a beggar, torturing orcs for info., killing werewolf babies, etc.).
Equipment: Put in a competitive 2-h bludgeoning weapon. Make Great Ax and Greatsword do identical damage, one way or the other (1d12 or 2d6). Explain more clearly weapon size with ranged weapons (what can be thrown by whom? What range do non-medium weapons have?). Put in a competitive bludgeoning "Bastard"-style weapon.
Make hand crossbows cheap and Simple weapons. This will not break the game.
DMG: Mass combat rules. Bonus if you have MCR in which pc actions make a real difference.
I may put more here as an edit later.