Hi, I've used movie salsa a little, I'm not saying its the best or anything but works and is somewhat inexpensive.

http://www.imagesalsa.com/MovieSalsa/

Also when it comes to taking time-lapse of clouds, I've found that 1 shot every 15secs is pretty good, however I wouldn't go over 30secs as I found that it shows to much movement and doesn't flow that nicely

Good Luck
Steve