I'm going to answer this based on my new location and what I *think* will happen to my commuting bike!

1) How do you keep your commuting bike in good shape? I might be able to keep my bike inside while I work, but what about commuting to other places?
I bought an older bike to commute on. At home we have a garage, but at work, it'll be chained to a bike rack exposed to the elements. Same would be true if I rode it to run errands, of course. Because of this, I didn't want to use my road bike or my old 'commuter' which is actually a touring bike. I hope to keep it in working condition by keeping it well lubed and fairly clean when possible. I don't expect it to ever be pristine. The bike I bought has some chipped paint, so I plan to seal those areas with clear coat to avoid rust (and leave the paint looking chipped...I don't want a bike that looks TOO nice out there!).

2) Did you replace the stock saddle on your commuter bike? Yes, immediately.

3) Do you use clipless pedals on your commuter? I'm considering an spd/platform pedal (spd on one side, platform on the other). Both of my commuters (my old one and this new old one) will have the same pedals you are investigating. I use the clipped in feature for longer rides and the platform for quick trips.

4) Is the maintenance cost for a commuter bike comparable to that of a road bike? Not sure. It was pretty much the same on my old commute. My commute was a bit tougher on my bike than my road rides, but I did WAY more miles on my road bike...so the costs and wear were similar. I expect that my new situation will be similiar. It's a tougher bike, but I'm putting it through a tougher situation...so it'll likely need equal maintenance.