youtube keeps telling me that my .mov files are not compatible after I upload them... don't know why (maybe because it's HD?)
Intel mac
How I understand it is that MOV movie files have an index in them that indicates where specific video and audio frames exist in the file. If that index exists in the beginning of the file, then Youtube can recognize it. Otherwise it plays dumb.
This application may allow you to switch that index to the beginning as Google/youtube seems to want.
http://renaun.com/blog/code/qtindexswapper/
Can't promise it'll work and I'd recommend trying on a duplicate of your original file first, but it seems to have been updated as recently as yesterday, so it might have a good shot of working for you.
It looks like it requires adobe AIR. Trying it out here on my test iMac for you.
EDIT: I installed AIR, installed the .AIR file from that dude's website and processed a file without and issue. Without having a file that has the moov index at the end, I can't confirm it worked, but the MOV file I uploaded worked just fine. I'd say give it a whirl and see if it works for you.