Besides fixes for a couple of 10.6 bugs, the biggest change is that all the features of VoodooPad Pro have been rolled into VoodooPad regular. The price of VoodooPad has been raised to the halfway point between the two versions as well. So you get all the power of VP Pro, while spending less.
So why kill VoodooPad Pro? It's about simplicity, and wanting to reduce confusion. I just wasn't happy with having 3 different versions anymore, and honestly I'm not happy with 2. I can see a day off in the future (not any time soon!) where there's just VoodooPad, and no longer VoodooPad Lite. You'd still be able to run it for free, but it would be a single binary and go into "free mode" after 14 days or so. I originally got this idea from what Red Sweater did with FastScripts (which also used to have a free Lite version).
If you've got some AppleScript or JSTalk scripts setup to use VoodooPad Pro- don't worry, you won't need to change those to point to VoodooPad. The Pro version is still being built, and is updated along side VP- but they are exactly the same, with the exception of the name. The auto update mechanism will download version 4.2 of VoodooPad Pro, and everything will behave exactly as it always has.