From what I recall, caffeine app predated the caffeinate command (which was only introduced in lion). Caffeine.app also disables sleep via a completely different method than caffeinate. The latter uses a IOPMAssertion which is the recommended way to do it because it is visible in `pmset -g assertions` whereas the former doesn't use that approach (I forgot how exactly it did it, there's like 4 different methods on osx to prevent sleep).
