Liam Howlett used Reason (among other things) to make Always Outnumbered, Never Outgunned. I'm not sure what was used for their latest work, Invaders Must Die, but it's likely similar software given their live setups for the last few years have been powered by several Macbook Pro's (along with other equipment).

Truly a master at his craft though. Here's a hacker who started making professional electronic music mostly the old way in the early 1990's, and has successfully transitioned into the digital age. If you've listened to Prodigy long enough, you end up coming across music they sampled in the most unlikely of places. It's like an endless easter egg hunt. I can't even begin to imagine how dynamic Liam's record library is.

BTW, if you've never seen them live before, you don't know what you're missing. Seen them three times already and they easily outshine NIN, Manson, and Rob Zombie in terms of live energy. The type of crowd they attract is energetic and intense. But bring a pair of earplugs if you don't want to go deaf. ;)

Edit: Check out Nekosite if you want to know more about the band: http://nekosite.co.uk/