I prefer a dark commute as well (other than the getting up early part ). Overall, I'm pretty comfortable with my setup:

-Front: main light is a Busch & Muller Ixon IQ. Battery powered German light that I LOVE. Nicely shaped beam and plenty bright for unlit trail. Right now, it's on my bars, but I have a fork mount that I'll try whenever my new bike shows up-- the fork mount and the cantis on my current commuter don't play nicely together. I also have a Flea that I run on strobe since the big light is solid only.

-Rear: Flea on the rack and some kind of little Knog in one of the vents on my helmet. Both running on different flash patterns.

-Passive: reflective trim on shoes, jacket(s), helmet, pannier. Reflective tape on the legs of my rack and reflective strip on my tires (more visible when they're clean...).

The only things I'm contemplating changing is adding some kind of annoyingly bright helmet light for the 6am zombie drivers and a more sturdy rack-mounted tail light (Flea is currently held in place by a velcro strap and a paperclip...). I'm on the fence about the helmet light since it really would be for about 15 minutes of apartment-to-trail distance in the mornings but I suppose if I can find something cheap and rechargeable I may give it a shot.