I commute on a folding bike and it works well for my route, i.e. 6.5 miles from home to the Metro train station, fold bike and get on train, ride Metro train for 10 mi., exit train, un-fold bike, ride 1.1 mi. to work.

My bike has 16" wheels, and for sure the ride quality is different from my 700C wheel bikes. However, the small fold size works well since the bike doesn't take up much room on the Metro. You don't say whether a train (or subway) is part of your commute, but if so, the folding bikes makes the most sense (unless your train has specific bike parking accommodations).

I have it set up to fit me well, and while I would never think about riding a century on it, the folding bike is remarkably nimble, very well geared (Shimano Nexus 8-speed) and easy to live with on a day to day basis. My bike is a DaHon Curve SL and I've added a rack (also DaHon) and a rack trunk. The only spec. change I've made is to replace the standard MKS pedals with Shimano SPD.

Attached photos of my DaHon in folded and un-folded modes!
Rick / OCRR