I'd go with a performance hybrid. currently I'm riding a Norco Volante (Canadian make)(linky)

Pros:
-linear pull brakes (like MTBs, have more power than caliper brakes)
-flexibility in tires (go as thin as road racing tires, yet up to 35c for more comfort)
-tire size/speed (700c tires for speed, with higher gearing than a MTB)
-position (more aggressive than MTB, but more relaxed than road)
-weight (lighter than MTB, heavier than road bike)
-frame flexibility (hybrids easy to suit up with full fenders, racks)

Cons:
-no shocks for very bumpy roads (some comfort hybrids do have shocks, but often you're extremely upright body position then)
-lack the aerodynamic position of road bikes (should you want to get into racing)


Mind you the fact that you're building the bike is a big factor too. A hybrid wouldnt' need much anything changed (just adding some accessories). Whereas for a stock MTB or road bike, you might want to swap components for commuting.

Just a few thoughts,
-xan-