This is not a new idea.
There are already several "commute timer" apps available for Android: The usual pattern I see is that they track your location over your commute to and from work, and give you arbitrary statistics based on that. (Total time, plot your path on a map, best/worst time, slow parts, fast parts, etc.) From here, they add various conveniences like starting automatically based on time+motion. Someone mentioned wanting an app like this in a forum post.
I found iCommuteLess and a paid app simply called Commute Timer for Android. They're both right up the alley of location-based ubiquitous computing (shout-out to ActiveCampus!), which makes me feel warm and fuzzy inside, but they're not what I want.
The apps I've found seem to use the GPS extensively, which doesn't work if you're underground. (On, say, a subway.) They (or, at least, iCommuteLess) are also filled with bells and whistles (read: bugs). Phone screens are underpowered and small, and lots of features means a slow, clunky app unless you are very clever and very, very good at UI design.
What I'm imagining is similar to what the forum poster described: a glorified stopwatch. You can start the timer, mark a midpoint (just like the "split" function on a stopwatch), and stop. It saves the history for you in some easy-to-read format. You can do all the number-crunching you want on the file. I specifically would note when I leave my apartment, when I reach the train station near my apartment, when my train arrives, when I leave the train station near work, and when I'm at my desk (plus the reverse).
No GPS means you lose all ability to automatically start and stop, but it also means less battery life (and of course the ability to use the things on trains).
I'll keep looking for something, and if I don't find it, I might have a go at writing it myself. I've been looking for an intro-to-android-programming project for a while.
Of course, if someone reads this (ha), and implements it first (double-ha), that's even better. You can't own ideas, man...
[Edit, 2013-01-03 21:12 EST: This post is already the second hit on Google for "android commute timer app". This doesn't bode well for there being an already-existent gem out there, just waiting to be discovered. Dammit.]