I would love to learn SuperCollider, I downloaded it ages ago but didn't have the patience. It's free though which is nice.
Max/MSP is used by quite a few people such as the guys in Autechre and Radiohead. I also like what I have read about Jitter which is part of Max/MSP now.
Reaktor is also widely used and would be great to learn.
And check out the Pure Data score for Hans-Christoph Steiner's Solitude down the bottom of this page. That looks amazing! Pure Data is also free.
Anyway there is a list of these types of apps here with a few more I didn't mention.