I ride my track bike both on track and on the road. While commuting, I like to have both front and rear brake which I have to take off for riding the 'drome. It's a drilled frame and fork, so mounting the brakes has not been an issue. I have the brakes attached to a set of cross levers that I can easily detach and reattach. Same goes for the calipers, all it takes is a allen wrench. I even bought single-pivot calipers which are much easier to mount while the wheel is already on the bike.

The only problem is how to attach cables to the frame. Right now I hook them up using a bunch of cable ties that I cut every time. Now, I am thinking of some sort of velcro-based strap system or, even better, attach the rear brake cable to a top tube pad that would itself be velcro based. Would this kind of setup give me any kind of problems?

just some velcro should do the job. it would be the fastest route..although I believe there are soe simple bold on cable olders for this purpose, check out the bmx forum, see how they all hold their rear bake cable down.

id say ditching the back break would take care of your problem.

Yeah, the only problem I see is your rear brake :-)
Velcro seems like it'd be perfect to me if you insist on a rear brake.

You could get a top tube protector, and just run the brake line underneath.

good point. i hadn't thought of that. sounds like that make be the easiest solution.