I don't tinker with game mechanics, I tinker with fluff. I take a look at the books I have and ask myself, "How does this (feat/spell/PrC/race/whatever) fit into my world?" and go from there.
For example, my campaign is centered around the concept of "no gods...yet" with the PCs having the opportunity to become some of the first gods. So how did I cram the cleric into that? All of the clerics, and they're relatively rare, are clerics of a philosophy instead of a deity. Another example: the Red Wizard PrC in the DMG. Pretty exclusive to FR you might think, yes? The named spells in the PHB...the names attached seem pretty GH, yes? I mushed 'em both together. The original Circle of Eight founded my version of Thay and created the Red Wizards to rule the land. At least one of the original circle is still on the current Circle of Eight, a thousand years later as a lich.
Also, and this was an important lesson for me, whenever I acquire a new book, I don't try to backtrack and say, "Oh yeah, this stuff was always here...you just couldn't access it because...uh..." Instead, everything in the new book is worked in as brand spanky new. The PCs get to be a part, for example, of the founding of the Nightsong guild or the party's bard is the first Seeker of the Song, or whatever. Races and monsters are little trickier, but when you have a nation ruled by semi-psychotic wizards, new creatures popping up isn't quite so difficult.
So, after too much rambling, my point is that you don't need to reinvent the wheel...just put the wheel on a different wagon.
Quentin
