I currently use a combination of
TourGuide,
nQuestLog,
Lightheaded,
TomTom and
MobMap as I have been doing what you wish to do.
TourGuide will check off all the available quests. nQuestLog tracks the individual quest (obviously) and links to Lightheaded. Both Lightheaded and TourGuide have a link to TomTom and MobMap fills in the gaps, for example if you cannot find the giver of the next quest in TourGuide, MobMap should help.
It's quite a few addons I know but they've served me well so far ...
N.B. I don't think TourGuide has class quests or PvP or City (or not all at any rate), but it does split the rest by zone/level. It will also check them off automatically when you turn in. Tekkub's own description is
here.