Good advice here ...
Last several systems I've built have been Intel chipset / CPU, Gigabyte or Asus MB, WD hard drives. Optical drives appear to be pure commodity. Always hated ATI video, so I'll stick with the crowd on Nvidia.
I did build one system with a Gigabyte MB and AMD CPU (3GHz dual core). It's my "home theater" PC, so nothing special except that the MB has HDMI output (that's real common these days). Runs tiny-XP and I went with AMD to keep costs down. The on-board video is ATI and that's really my only complaint about that box. ATI video has always been finicky for me and this one's no exception.
I think the AMD stuff is really 100% compatible these days. A lot of folks prefer it over Intel, and it is a lot less expensive.
Haven't built a new i3/i5/i7 system yet, and it'll probably be awhile; don't need any more than what I've got.
ETA: And Newegg does rock...