To mount a motherboard in a 1U case, you need one that's specifically designed for it. A special CPU cooler also is required and you need several high-speed and noisy little fans to cool it properly. Unless you have a computer room, you probably want to stay away from a 1U case. Only one or two hard disks can be installed.
2U is easier as long as you carefully select the controllers (full height won't fit), but it will be nearly impossible to find one to install 6 or more hard disks. It's a lot easier to use a 3U case and lots of good cases are available, e.g., http://www.gtweb.net/j3125.html.
A good P45 motherboard like the Asus P5Q Pro, the Asus P5Q Deluxe or the Gigabyte GA-EP45-UD3P should meet your requirements. Since they have two Gigabit Ethernet ports, you can configure them as a router. If you need more ports, then you can look at the P5Q Premium or the GA-EP45-DQ6. You'll have to install a WIFI adapter or buy a motherboard that requires DDR3 like the Asus ASUS P5Q3 DELUXE/WIFI-AP.