running wire perpindicular to floor joists

You may want to avoid drilling, but the strength is basically at the top and bottom. Holes in the center essentially don't affect strength.

Another way to do the wiring is to put multiple circuits in PVC or thinwall conduit and run them to J-boxes at appropriate locations. (You need to know what the derating rules are.)

Most inspectors can be real helpful if you basically know what you are doing.

I was just in an attic in a friends house. The house is 5 years old. In the attic, the wiring for a couple of lights, outlets etc is just romex and it run over the top of and perpendicular the roof cross ties or whatever you call them that are at about or just above head level. I didn't really check, but I don't think it's even stapled down at regular intervals. It didn't look Kosher to me.

Regaring Limp Arbor's situation, I always thought you could just nail up some shingle rib perpendicular to the joists and then staple romex to it. I'm curious why the inspector wanted it covered in sheet rock? Wouldn't seem to be any different than stapling it to the center beam, no?

He only said I needed to cover it if it was stapled underneath and perindicular to the joists. If I stapled it to the side of a joist or to the sill plate no need to cover it. I also could drill through the joists and not cover it.

I guess the theory is that if the wire is running through holes in the joists no way it can be pulled down. And with support underneath the wire also less likely to be pulled down than if it was just stapled.