I don't allow godless clerics, HOWEVER, I do allow the Mystic class from the Dragonlance setting for Divine casters who want another option.
I view most stuff on a case-by-case basis. While I'll allow the "rogue-paladin" and "rogue-cleric" PrCs from Complete Adventurer, I will not allow the Order of Illumination. I'm sorry, but you can't be Lawful Good and still destroy an entire village just to root out 1 demon.
Evil and CN PCs I don't care for.
I also don't like the +LA races, it sucks to keep track of and hasn't become an issue because most of my players have never wanted to be a level or more behind.
A lot of the restrictions I've seen here, though.. seem really overboard. I can't believe so many people would feel the need to "dumb-down" so many class abilities. Adjusting PrCs are one thing, but screwing over the core classes would just make me want to say "eh, screw it.. I'll just go re-play Baulder's Gate if I want a DnD experience.." heh. So, why do it? I'm really curious. Sounds a lot like one of my friend's Dad, who DMed a game for us during 2nd edition and though "all arrows should do 1d6 and weapon specialization for a fighter was much too strong".
Rather than jip my players, I'd much rather make some more difficult encounters.