I'm also pretty sure that there are some issues with cutscenes under OpenGL, especially with Sync (non-MVE), but I think those got kiboshed in later builds. (RC's for 3.6.9). Under FSPort the only cutscene you should conceivably have is the final one (after you nail the Lucifer in the subspace tunnel.) Dunno about FS2, haven't yet played all the way through it as I'm debuging mission file inconsitancies and minor little nit-picks.
Sync had cutscenes? Now I'm a little..... angry. 
Anywhere they can still be found?
As for FS2 cutscenes, the important ones are the Bosch monologues (I think there're 4), and the ending su-...... no, I won't spoil it for you, but believe me you want to see the ending cutscene. They cutscenes are located on the discs themselves, but if you got a download, your best bet is to look for a downloadable FS2 cutscene list. I think Karajorma's FAQ has links, they were down a long time, but recently I think they were fixed. A link to the FAQ can be found on the "Related Sites" tab at the top of the site.
No, I've had the game since '99. Back in '01 the original discs got damaged and I thought I'd never be able to play them again, but I sent the discs off to Volition and they sent me brand new ones!

I've just waited till now to do the SCP thing. I guess the multiplayer scene is only around here because I think Volition's server is gone, right? Back in the day, I used to hang out with these dudes who called themselves the Beer Drinking Hell Raisers, but I never joined a squad, I always got slagged.
Anyway, I don't really *need* to see the cutscenes myself since I know what they are, I just want to have them cause I like them. I'm also giving some of my friends copies of the game IAW the software liscence agreement, and I noticed that if you copy the disc, it won't play the cutscenes, even with vanilla FS2. So, I'm using the SCP to not only give my friends a newer shinier version, but to also let them see the cutscenes.
So, the cutscenes are on Disc 2 and 3. I actually put the contents of these discs in seperate folders, and it's a good thing, the discs were starting to look pretty scratched. I found out you can install the whole game from these folders, but the cutscenes won't play at all. So, I guess I just take the movie files from the discs, and put them in the data folder in Freespace2? No need to convert it to .avi or do anything with the SCP launcher? I'll check the faq, though. Thanks guys!