All software should be as awesome and just work like this. I've used video encoding software in the past like Nero recode and it wasn't half as intuitive and easy to use as this!
Finally found the perfect solution to recode all the flv video files I have laying around to ipod compatible format. I have QuickTime pro but it doesn't read flv files by default. Besides handbrake is pretty fast and uses all 4 cores @ 100% from what I can see.
I used the following guide: