If you're prepared to pay for it, there's Cubase SE/SL/SX or Sonar/Home Studio. If you're not prepared to pay, I will as always recommend Synthfont, which is donateware (meaning: you may, but don't have to pay). There's some info here .
N e one out there know a good program to record my notation files into mp3 or wav other than kontakt.
Helpful to know what software you are working with, and what sound card. For instance, with Sibelius, you can create wav files, and using Windows Media Player, convert them to mp3. This is one of a large number of ways to do it. I generally use Sonar for the wav files, then Cakewalk pyro for the conversion to mp3.