I'll second Personal Brain - its mind mapping software that allows uploads of files, etc. I find it a bit easier to get my 'stuff' into Brain than into Evernote ... but I do use both...

I've been giving public transportation a shot - but I do think it is more expensive than driving. I drive a '99 Honda Civic that gets great gas mileage, has ~ 125k miles on it, and is my 'go to' car for city driving. I drive to the Commuter Rail (about 4 miles - walking is possible, but I'd be a sweaty mess ), pay $4/day to park, then about $4.25 one way on the trip itself... Driving is about ... $40 a month, but that obviously doesn't include insurance, wear and tear, etc. I'm still giving the commuter rail a shot - but the convenience of driving does win occasionally.

Coming from a data mining background, InforSense's platform allows you to not only manipulate your data, perform calculations (and data mining) but then visualize your results in an AJAX environment. You can call open source apps like R and Cytoscape directly from InforSense's workflow building application, so none of your pre-existing work gets discarded.