No need for a suspension fork on the mountain bike to handle the irregular surfaces. You can accomplish the suspension through running fat tires with low rolling resistance such as Schwalbe's Big Apple (26 x 2.35 and available directly online from Schwalbe) and maybe a Brooks sprung saddle like the Champion Flyer (Can be had for $59 on the net). Or, a more expensive route is the Thudbuster suspension seatpost at $90 - $125.

You could also go with a 700c mountain bike set up to have the best of both worlds for commuting. Big hoops and fat tires (again - Big Apple's at 700c x 2.0 or 700 x 2.35) would really soak up the hits of uneven road surface. You wouldn't even need a suspension fork - you could run a rigid fork (such as Surly's). Great steel frame from Surly available called the Karate Monkey. Build up your own commuter. Or Gary Fisher is a production company with the two-niner hybrids (come with front suspension) where you would probably want to get the one with the lockout fork so when riding the sections where the road is smooth you could lockout the fork and not waste any power to the drivetrain.

Me? I've got tandems, recumbents, mountain bikes, Surly Karate Monkey, Big Apple tires - I'll take anything to work on my commute cause I love it all. No fenders or racks though. I wear waterproof pants and jacket when need be (also work well in winter to block out the cold) and carry all my office goodies on my back. Been doing that for 9 years now.

Newest commute set-up is a Burley Koosah (like 2 days old) running Big Apple 26 x 2.35 in the rear and a 20 x 2.35 up front at 40 psi. Big volume, incredible rollers and all the suspension I could ever want. Monday will be the maiden commute voyage...

BB