iSubway Maps for 24 cities are available for free download to your iPhone or iPod (except for the mini and shuffle, because they don't support photos)--and it's compatible with both PCs and Macs.
Sadly for William Bright, creator of this very useful site--while living up to his name--he's been sent cease-and-desist letters by the MTA in NYC and the BART in San Francisco.
The BART has gotten on top of issuing their own version of the iPod maps, and also has schedules available. MTA looks to be doing it more for the money because they're trademarking and licensing their route symbols. Bright has been recreating the maps to get around copyright issues.
-Thanks to our friends over at GeekSugar, where we first heard about this site, for saving us from formatting the picture ourselves!