I ban stuff on a case-by-case basis, but most of the time it's only if a player asks about something or mentions it; I don't waste my time combing through books and analyzing every spell, item, and class to decide if it's broken, so I just inspect the ones a player actually considers taking (before deciding if they will be allowed to take it or not).
I usually allow anything that I have direct, personal, hardcopy access to, within certain limits, and then I ban any parts of those materials that I deem overpowered or unsuitable (like: no, you will not play a spellfire channeler in Greyhawk :\ ; and the frenzied berserker isn't a prestige class, it's a barbarian by another name, so no dice), if they aren't easy enough to houserule minor changes for.
There are only a small handful of things I outright ban from the start (like frenzied berserkers, forsakers, foe hunters, a few spells, a few magic items, and most everything that isn't in a physical book I own or can borrow). There are many 3rd-party books though that I'll just ban outright if the player intends to use them (I've seen more 3rd-party books used to break games than I have WotC materials; Mongoose's spellbook-thingy, I'm lookin' at you...
). I don't have a high opinion of WotC in this regard either, but higher than most of the other publishers, and at least in 3.0 books there was little in need of powering-down from any given book (barring all that Forgotten Realms uber-power brinksmanship). Many things I'll just make a quick and dirty houserule for, if the players encounter them or want to use them (if I deem them too unbalanced; minor imbalance doesn't bother me).
I rarely allow anything from books designed for campaign settings other than what I'm running at the time, and I rarely allow monster PCs (but I'm not intriniscally opposed to them; just would rather not see many in campaigns that are intended for a more civilized/social bent; I have no problem with running or playing a monster-centric campaign, but haven't had the chance for one yet).