In the I-codes, holes can be drilled through joists. The holes must not exceed one third of the joist's depth, and must not be any closer than 2" to the top or bottom chord.
As far as wiring goes, you need to avoid bundling. I'd have to dig for code language to substantiate this, but I'd limit it to 2 or 3 wires per 1" hole. The less, the better. Drilling a few smaller holes a few inches apart will always be the best way to go, as opposed to pulling several wires through the same hole.
Up to four cables before you need to be concerned about derating.
Sometimes I feel like if I answer any more questions it is like someone trying to climb over a fence to jump off a bridge and me giving them a boost.
Answers based on the 2008 & 2011 NEC.