I don't even try to track commuting costs because it gets too complicated. First, I never buy complete bikes. I buy frames and then have them built up with parts I've collected and/or swap parts from other bikes. Eg, I got a new Salsa Casseroll last spring and only paid $500 for the frame, fork and rack. I had the bike built with parts taken from another bike with a few new parts (eg, headset, stem, etc.) that I got from the bikeshop. My out-of-pocket cost was about $800, not including parts I already had, but the bike is probably worth $2,000 in replacement value.
I've put 3,500 miles on the Casseroll since I bought it. So is the cost per mile 14 cents ($500/3500), 23 cents ($800/3500) or 57 cents ($2000/3500)? Further complicating matters, I recently had to replace the rear tire, which I already had on hand from a previous bike but originally bought for about $25. I replaced the crankset just for the heck of it, and got a new wheelset for my birthday.
To simplify matters, I figure that I'm saving about 50 cents/mile by commuting because that is the approximate federal mileage reimbursement rate, which takes into account gas and maintenance costs of driving a car. By that formula, commuting saved me about $2,150 last year and I probably spent that much on bike stuff.