Since: Apr 03, 2002
I have a rackmount case, it's 3u high and I don't have any heat problems at all and only have one or two internal fans. It's pretty quiet as well. The rackmount case I have is here www.dealsonic.com/skyhip194ura1.html it's reasonably priced and very well constructed. As far as a motherboard, well, by the best Mobo for the CPU you want. Build around a CPU, not a Mobo. I prefer AMD for it's cost/speed ratio, it's not as fast as Intel, but it is so much less money one can usually afford to buy a better one.
It's hard to get a Mobo without a built in sound card, network jack, and no even video built in is very common. So, when you buy, buy a reputable brand (I am a fan of Asus myself) and make damn sure that the BIOS allows you to disable the sound chip, and maybe video chip if you have a fav video card. If you don't plan to do any video work, a built in video chip using a good chunk of shared RAM could likely do the trick. If you go that route, be sure to get at least 1 GB of RAM so you can share 128 MB or so with the video chip.
The speed RAM you buy will be dictated by the mobo and CPU you choose. As far as hard drives go, you will likely have SATA drives on any system if you build it with all new parts...get one with high RPM and fast seek time.