The 12VDC power supply is sufficient to power both the lights and a Netduino or Arduino. Just desolder the little controller it comes with. There are 5 wires, but the colours are not intuitive. For example, the black wire is +12VDC and blue is ground. With a few transistors and resistors, they are really easy to work with.
Also, if you're into Ikea 'hacking' then here's some fun with the Ikea LILLABO train set: http://blog.jgc.org/2010/01/more-fun-with-toys-ikea-lillabo-...