+1 on the GPS
I'm a programmer, and have thought about this kind of thing myself. Realistically though, using a computer to collect the data won't offer any benefits since you can't use it while riding. You get the extra weight and complexity of something designed for general purpose computing, and the only data you could collect is speed at different time intervals.
A GPS is smaller, has better battery life, is easier to use (you don't have to boot it up, or hope that the shock of the bike bumping on the road doesn't shorten the life of the hard drive) and collects speed, location and altitude at different time intervals. When you no longer need to collect data you can just turn off the data collection then turn it back on when you need it. It would be way less hassle then hooking up your computer every time you ride. You can move the data to a PC later to do detailed analysis if you want to.
The only other thing that may make sense would be to use a PDA with gps to do collect the data and analyze it later on.
Using a GPS would require almost no custom software, collect way more data than a normal bike computer and would be more durable.
If you REALLY wanted to use your bike computer's magnet couple with a computer you could use a PCMCIA card with an Analog to Digital converter and collect the pulses that way to find the speed. It would be most effective with a real-time operating system, but with something that simple I don't know that it would matter too much.