It depends...
I think I've used bits & pieces of elements here & there, like metamagic feats, PrCs, etc., but nothing across the board all the time. There are certain PrCs that I don't use at all (too specific to a particular setting, or they introduce elements that I want to keep out, etc.), certain feats, etc.
However, I don't think I've really used the NPC stats in the DMG at all, much less in any other books, either (like Races of Stone or Enemies & Allies). More often than not, the pre-gens just don't fit w/ my style of campaign at all. Then again, I prefer to use have as few NPCs with levels in a PC class as possible (unless the NPCs are established regular characters, cohorts & other PC-linked NPCs, or notable foes/opponents/villains); I'll have the setting populated more with NPCs with levels in NPC classes instead. More or less to emphasize that the PCs are not "average" by any stretch of the means--the PCs have a greater chance of finding a Warrior rather than a Fighter, an Expert instead of a Rogue or Bard, or an Adept rather than a Cleric or Druid much less a Wizard or Sorcerer.
I tend to use PrCs fairly often, but mainly to fit a concept I have in mind rather than for a random element. The NPCs w/ PC class levels and a PrC or 2 have been designed that way from the beginning: the class combos are made to maximize their abilities alongside the PrC. An elf or half-elf bard/arcane archer, so the character can cast a fair # of spells (instead of being stuck w/ just some 1st-level spells for the 1st-level arcane spellcaster class, & have a bunch of fighter levels heaped on), cast those spells while wearing light armor (and realy use that high Dex bonus to full effect), and have some nifty other abilities in addition to the arcane archer abilities. Same thing in mind with an elf swashbuckler/wizard/bladedancer w/ a rapier (high Dex, high Int, spells in light armor, etc.), a cleric/sorcerer/mystic theurge (high Cha for arcane spells & turn undead), a ranger/assassin (use those favored enemy bonuses along with the death attacks), etc. However, all in all, it's so that the NPC really fits in with the concept that I have in mind--the NPC's well-known for doing X, so the NPC's abilities are focused towards doing X, and their abilities in W, Y, & Z aren't as good.
And, more often than not, I pretty much need to build those NPCs from scratch rather than lift them straight out of an existing source.