Most of these are setting specific to my game world of Orea and some go back...ooooo...a decade or two. But I suppose they would be considered "houserules/homebrew" all the same. Since it is the only setting/world I game in, I suppose all of them are.
1) Max HP at first level. Following levels you can take 1/2 your HD automatically or roll...but if you roll less than half, you're stuck with it. Con applies as normal.
2) Spontaneous casting for Clerics & Druids 1st & 2nd level spells.
3) Spontaneous casting for Mages cantrips & at two spell levels lower than your highest. (A 5th level wizard can cast 3rd level spells. So she is able to spontaneously "remember" and cast the 1st level spells in their book. At 7th level, they gain 4th level spells, so 1st and 2nd level spells can be chosen on the fly. )
4) Orea's Barbarian culture/human tribes. Barbarian is a class and race with 7 (?) possible tribes of varying flavor, totemic animal, ability bonuses, special clan weapons, etc.
5) Orea's worldwide Druidic Organization (the Anicent/Holy Order of Mistwood) with special items and abilities built-in.
6) Several "Prestige" or "Specialty" Orean classes, mostly in the clerical/divine area. Of particular flavor and use in play over the years include: The paladinic order of "Redstar Knights", the "Gilean Protectress" and the "Witch-Priests of Manat."
(Yeah, it's a lot of/high magic kinda setting

)
7) I don't know if its a house rule or just carried over from somewhere I do not recall, but any class/character can "bandage/stabilize" a character at negatives. Obviously, if they have some sort of healing skill, they can do more, but anyone can remove themselves from combat to assist a fallen ally (and naturally risk attack in the process). Can't add any HP back, but can "hold you"/stop the descent to -10 until more skilled help is available. Healing magic will work as normal, of course.
As kind of "unspoken rules" (at least I haven't had to make them spoken rules in a verrrry long time), but will be brought up as necessary: the already mentioned "No evil characters", "No disruptive characters" (you can get across that you're introverted or selflish or what have you without detracting from anyone else) and "Come up with how you guys are together." As DM, I am willing to fudge this last one for players who "just don't know/can't figure it out" or have a first session scene in mind to get themselves together. Sure, I can allow that...usually. But at least a few of the PCs should be acquainted before play starts.
That's about all I can think of right now...I'm sure there are others.