Hey, I have used Java significantly in school, along with Visual BASIC, FORTRAN, and a little C++. Of the four, I would have chosen Java as well for programming my robot, and as for building your own MoBo, you can do that if you want, but you might consider using something like this here.http://www.logicsupply.com/categories/mainboards
I was considering using this very same board, or perhaps a Nano- ITX form factor. You can get a wireless card adaprter specifically for this board, meaning you can theoretically make your robot utilize the internet or at least a network for operation. The possibilities are endless.
Oh, and you might consider a SSD as opposed to a HDD simply because seek times are faster and the form factor is more low profile. Up to you though.
Cheers, and good luck mate.