You guys who haven't used the NPC stats are missing out. Those things have saved me so much time I can't tell you. Even if I just use them as a starting point, they're great. A lazy DM's best friend.
Though I'll be bad and issue a "me too" on all the reasons people state for not using prestige classes, metamagic, and templates.
Metamagic in particular just always struck me as a good idea that didn't work out so great. It could have been a system that made lower level spells useful for a caster's whole career. Specifically a metamagic feat that incresed the cap on spells the affect a specific number of HD would've been awesome.
Prestige classes have just never appealed to me in D&D. As a player I always considered that they're too much of a pain to qualify for, and both in meeting the qualifications and then taking levels in the prestige class I usually had to give up too much from the base class. I like the Advanced Classes in D20 Modern, but those are much easier to qualify for and since D20M's base classes are only ten levels anyway, you're not giving up nearly as much base class progression.
Edit: Oh, and Merak, I've used some of those things on your list as a player. I griped a lot when 3.5 took away the Refocus initiaive option. Almost always used it with spellcasters. My monk character tried tripping and disarming a few times, but when none of the attempts suceeded he went back to using flurry of blows instead. I had a character who would've used the Aid in combat action, except it's melee only and he was a low-Con archer. I looked for chances, but it never happened.