Nuke

It's an excellent, and incredibly deep, package designed to assemble composites that are not commonly found in low-budget films (multi-stream renders and dozens of layers). I think it's over-kill for the indie filmmaker because it can take a long time to master, and is designed around a complex pipeline that's typically supported by a full VFX crew, in several departments. That said, I mess with it every day but would never ever consider myself expert.

For simple stuff I often jump into Motion and slap a few layers together.
 
I use Shake which also uses a node based workflow. Once you wrap your head around it, it's nearly impossible to use the layer based software again… really natural feeling once you get into it.
 
Nuke also runs over $4k/seat, so I can't see it being particularly practical for the ultra-low budget film world. The power of something like Nuke isn't much use if you don't have a person/team who are experts in it, and people like that don't generally come cheap.
 
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