UPDATED POST- UPDATES IN RED
Back in May, PM Summer at Cycle*Dallas called attention to the NCTCOG "alternate commute" site, shown here. I did then and still do use that site regularly to track my commutes. It's somewhat lame, as pointed out by multiple people, but my employer gets gold stars as a participant, and that's a GOOD THING. What's more, I export the results to Excel and can tweak them easily thereafter. It's how I know that my projected 5K mile 2009 commute point is on November 12th. It's also how I know that another, currently secret, major milestone is coming up.
However, there are lots of other sites that you can use to track your bicycle commuting. Locally, DORBA has it's "Commie Monitor." It's highly regarded by some, though recent tweaking has given it a few problems. Going further abroad, Cateye has sponsored a commute tracking site here. Not to be outdone, Civia has done the same, shown here. I've also heard that Trek has a commute tracking site, though I can't find it. There are more. ChipSeal, in a comment made not long after I posted this, noted he uses bikejournal.com, shown here and I suspect he's onto a good site since he knows, within a few yards, just how much mileage each of his bikes has accumulated. I'm sure there are lots more.
The point is - track those miles! Just make sure you can save the stuff to your own computer and customize the results. Beyond that, simple stuff will really work just as well as the complicated tracking. If you have an "engineer" kind of personality, you'll soon be working to increase the slope of your mileage curve...