Problem with cubes:
1. space
2. space
3. space
4. Space so its VERY LOUD
so not having space means... cluttering of wires, hard to get connectors in.... hard to mount extra fans to help cooling in... Limited range of parts you can use in a cube case...
Options if u really need a cube case:
go mobile cpu with mobile board variant.... very expensive but low heat means higher clocks and less cooling required... 1 have one from AOPEN.... its the imac wannabe clone that uses a doltan CPU.... they have ones for core2duo meron if u want that route.
I wouldnt go cube... there usually built less sturdier then a case, also be prepared for war scars!!! meaning ur gonna cut yourself or something when u build it.
EDIT::
AHHHH u want to make a HTPC... Get a HTPC CASE instead... Those are much better.. Good ones are from silverstone. HTPC CASE for the wise! instead of cube!