I'm planning on getting a Kenwood DNX9960 head unit, but that's going to be a while (I got tires, wheels, and a few other exterior mods I want to do first). So what I'll probably do is get a line-out converter so that I can run an amp and whatever speakers and subs off of the factory radio for a while. Then when I get the money later I can remove that and hook everything up to the new head unit.
So I think I'm going to start out with this sub:
Rockford Fosgate® - P3SD412

And then move on to these speakers (along with some tweeters probably):
Pioneer USA - TS-D6802R - 6" x 8" 2-Way Speaker with 260 Watts Max. Power

But does anybody have a specific amp they would recommend? I just have no idea what I'm looking for there.

But I've got a friend who said that he's got a RF shallow sub in a tiny box under his seat, and our local stereo shop (who is very reputable) told him that rather than porting the box, it's cheaper to use that polyfill stuff and it works just as well if not better than porting.