When I went in 1995, my Let's Go: Spain said Girona was "a world class city, patiently waiting for the world to notice" and they were 100% right. I was just there in September 2015, and while it was still wonderful, the world has definitely noticed - there were tour groups galore (although, as said above, they are concentrated in just a few places). If you climb up above the main drag where the tour groups are, you will escape them easily (and it is a climb, but you then arrive at the cathedral entrance level, rather than at the bottom of steep stairs to the cathedral).
The cinema museum is different from most others, in that it's extensively focused on precursors to the movies (persistence of vision toys, lantern shows, and still photography), and only has a small amount on movies themselves. For this reason, I found it highly worthwhile, but those looking for a more conventional movie museum (like the ones in Astoria NY or Berlin) may be disappointed.
I was only there for a daytrip each time, but an overnight sounds great (I wish my recent trip there had been longer).