I'm having trouble reading the CDs for the copy of Freespace 2 that I own. It's a "Sci-Fi Sim of the Year" edition, which claims to add "over 20 additional missions."
If I just bought the GOG version instead, would it include these 20 missions, or am I better off trying to read the CDs?

I would say buy the gog version since it will run on your system (XP, Vista) and you could search to see if the missions are on the CD in their own folder.
I am not sure if the gog version has the additional missions; I wold doubt it though.
Peace

Thanks for the info. It turns out my CDs just needed a good cleaning, and I now have backups just in case.
@Faithful: Once I'd gone to the trouble of getting the CDs readable and imaged to my HD, there wasn't much reason not to just install the copy I already own. Since I'm planning to use the improved open source engine anyway, all that GOG would be providing is the same data files as on my CDs. Plus I bet the gog installer doesn't make you watch a lowres trailer for Descent 3 ;)
It does look like you can probably copy the additional missions to a GOG copy (data/missions/*.fs2, it looks like), but again you have to install the CD copy anyway to get at them. If anyone's curious what these missions are, it doesn't look like it was really anything worth worrying about. From the readme: