Wipeout is great for the whole family. And what makes it better is that female host is really hot... The Middle is pretty funny too. I mentioned that I like that show and got flamed for it a while back.
I don't think there's that many shows that fit the mold of Monk. Maybe House but to a 12 and 6 year old some of the weird symptoms could really freak you out. If you have USA network, I would suggest Psych.
Bones - absolutely not. there is a ridiculous amount of gore and explicit decaying flesh. Any between the hours in which kids usually watch tv should be good. Television station follow guidelines as to what they can broadcast. So if you watch tv with them before 8:30pm, then you should okay with the content.
I haven't watched in a while, but Warehouse 13 on SciFi was pretty good, and seemed to be completely clean.
I forgot how funny MONK is. Watching the George Alexander as a P.I. episode. Man, GA is awesome. He is hilarious.