Really the whole rule set.
One aspect of 3.5 that I really like is skills. I'm a little peeved at the 4e skill system since it basically means that anyone of a certain level who is trained in a given skill is equally as good at it as some other shmuck of the same level. The 3.5 skill system allows for characters of equal level to specialize in specific skills while dabbling in others. This feels very realistic to me, which I like. It allows for a lot more variation frm character to character, even if they're a similar build.
Agree with both of these posts, for starters. Especially the skill system. That was the change that pissed me off the most in 4E.
Other rules (if another edition did it first, my apologies. Barely played 2E and nothing earlier):
-The special attacks section of combat rules, with (arguably) clearly defined rules for many of the things you'd want to do in a fight other than attacking the foe for damage.
-Movement rules, and the tactical uses thereof. Whether it's the ability of archers and mages to 5 ft step away and continue fighting, tumbling options, using spells and powers to nearly immobilize enemies just from difficult terrain, all great stuff.
-Multiclassing freedom unseen before or since.
-Readied actions. Many hate them for slowing things down, I always loved them and wished it weren't so obvious when someone was choosing to ready so as to make them more viable. It's amazing how useful it is in a duel with an aggressive foe to ready (move out of the way). They charge, you step to the side...their turn ends, you go now because your initiative changes to just before the other's, and he completed his action after you...you 5 ft step back in to melee range and full attack their (penalized for charging) AC. I love it! A lot of people also don't seem to realize you can 5 ft step as part of the readied action if you didn't move on your turn *devious grin*
-The availability of wands for widespread utility casting.
-The fact that everyone plays by the same basic rules, there is no metagame-y diffences imposed on the NPCs over the PCs.
-That the rules, and the fact there are so many for various things, reduces DM fiat to the lowest level of any edition IMO. And I think that's nice both for the players and the DM. I know when I'm DMing, I hate having to make up rules and DCs on the spot. Mostly because I worry too much if I'm being fair when I do so.
-Uniform levels and experience, and no more individual xp rewards in the standard rules. These were both really annoying to me about 2e, I'm glad 3e got fixed these issues. I don't want the Rogue to be 3 levels higher than the others just cause his class sucks, and I also don't want rules that encourage him with xp to go behind the party's back to steal things for himself. And certainly, it's nice to not have to deal with:
Party: "We're selling the scroll for money."
Wizard: "No! I can get xp for scribing it to my book!"
Party: "But, it's Mordenkainen's Seeing Eye Dog, you'll never use it!"
Wizard: "I don't care! I want the xp!"
-Instead of merely enforcing equipment restrictions on classes, 3e gives "reasons" -- ASF, druidic oaths for metal armor (but not weapons, yay!), etc... -- and often allows for feats and magic items to get around them (iron wood spell, twilight armor, armored caster feat,Spellsword class...).
Please don't sidetrack this into an edition comparison thread. That way lies madness. Just stay focused on the positive and give me the good stuff!
Sorry. It's hard to say why something is an improvement or better than the "improvement" without talking about other editions. I'll try when I think of more rules to post, though.