yea, the problem with stuffing things into small cases is that you run into size constraints.....when I put a computer into my scanner, I went with a fully integrated nForce motherboard because I knew I wouldn't have room for a video card, or any expansion cards for that matter...
Once you get the expansion cards under control, the next problem is the drives. Normal 3.5" hard drives don't post much of a problem, but you can use a 2.5" notebook drive if you want. What causes the most trouble is the cd-rom drive.....you can get a notebook drive with IDE-adapter for $30-$50....personally, I would not recommend the one from directron.com.....it's the cheapest that I found, but when I tried to use it it fried up on me for no appearant reason....it's still in there, but it's being used as a support for the hard drive, lol. I found that sharing a CD-ROM from across the network works just as well, hehe. All I did was have a cd-rom and floppy hooked up in order to install the OS, then I unplugged them and closed her up......she's been running great ever since.
These kind of mods are pretty difficult, but VERY satisfying when you finish them, hehe. My advice would be to plan everything out. Getting the drives mounted securely is the hardest part.