I think both FL Studio and Reason can be configured as the default MIDI playback device. To send MIDI messages to either from VB.NET, you'll need to PInvoke the midiOutOpen, midiOutShortMsg and midiOutClose API calls. Here's a link to code samples:
http://www.answers.com/topic/midioutopen
They're for VB6, but they should be easy to translate to VB.NET.
I know FL Studio can be "driven" from a plugin authored for FL (or a VSTx plugin), but I think these are always written in C or C++.
Edit: I just learned that Windows Vista dropped the MIDI Mapper (which would have made setting up FL or Reason as the default MIDI device simple). Amazing. Here is a link I found with an alternative solution:
http://akkordwechsel.de/15-windows-vista-und-der-midi-mapper/
I just tried it out (it's just a *.CPL file that you double-click to run) and it appears to work (although the GM Synth is the only option available on my laptop, so I'm not sure if it will pick up FL or Reason as choices).