Mocoso used to have an Atom pre-built that wasn't a bad deal, but to be honest if I were you I'd put together my own.
I have used the E350M1 for a few things, and it's a wonderful chipset. That being said, If you plan on running any of the big three frontends (Ride Runner/Centrafuse/OpenMobile), you're either gonna need a beefier system, or decide if you're ok with it being a bit slow to load/slow graphics.
SSD is a must for both speed and durability. They're getting fairly cheap, especially if you go with the lower speed ones (OCZ Agility for instance vs Vertex).
Memory: 2gigs is plenty, but if you plan to hibernate, 1gb might be faster. Not sure how win7 does it.
Case: Mocoso's case is compact, and generally decent. I have one, and I like it.
PSU: For the E350, a M2ATX would be more than sufficient.
Wifi: Generally just a USB dongle would be adequate.
GPS: Correct. I have a 353, and love it.
Bluetooth: Random generic USB Bluetooth device should work.
What screens are you looking at, and what kind of space do you have to work with? Can you do a double-din screen? IMO they look much nicer than any flip-out, and are generally more reliable.
As for websites to purchase things, I use newegg.com. They're fast, and I've never had issues with them.