When I try to run FS2 It says that "FreeSpace has detected that you only have 0MB of memory." blah blah blah.
I've tried compatibility mode, still doesn't work.
I'm Using Windows XP professional 64-bit with 4gigs of ram. I still have over 3gigs available.

Some 32-bit programs don't like 64-bit operating systems and 4GB or more memory. Try removing 1 or 2 sticks of memory, so you have less than 4GB and see if that works.

I've Used the MD5 Checksum checker and it's showing up as a different number than what is in the sticky. I've downloaded the file 3 times and Its the same thing. Could that be part of my problem?

I dunno. If the MD5 Checksum was really off, you shouldn't even be able to install it at all.

Yeah, I forgot about doing it that way. I used to have to do that when I was still dual-booting Windows 98 and XP and had to limit 98 to only see 999 MB RAM for most programs to even work. I never did find a way to do that at the program-level though...

Do you know how it works? ATM I have 2 sticks of 2gb DDR2 ram.
Does it just see a portion of each stick? Or only 1 stick?
Basically I'm wanting to know if it is disabling Dual Channel.

As far as I know, it would be a portion of each stick. Dual Channel works on a similar principle to a RAID 0 setup, meaning that the computer puts the RAM in parallel to double the bandwidth. This will put about half the workload on one stick and half on the other. Even if you limit the amount of memory that Windows sees, it will still follow the same principle, just each stick only being used partway. Dual Channel also works at the BIOS-level, so Windows can't mess with it and disable it.

You can also use Freespace Open. I have 8GB of RAM and it works just fine for me. I think you can even use Freespace Open with the old graphics, if you want to experience the game that way.

I have this same issue. I have 8GB of ram (4 sticks). I don't think taking them out physically is a good thing. Has anyone had any feedback from GOG support on this? I don't really want to dual boot (via boot.ini) my system either, though it's nice to know there's at least a working alternative that doesn't involve case-surgery.
Thanks.
Update - Nevermind! For some reason the Boot.ini method actually causes my system to reboot when selected. I'd really appreciate any help on this. :(

Don't know what GOG have done with the retail engine, but at least in the good old days, it could only detect up to 2GB of RAM. Any more and it would start counting it backwards, so that you'd get warnings of 0 or even negative amounts of RAM.
The FreeSpace Open game engine can handle large amounts of RAM without problems.

Yes, but it's only Freespace 1, isn't it? Or am I mistaken? I am playing (or trying to) Freespace 2...

http://scp.indiegames.us/mods.php
It has a installation wiki on how to get it all working for freespace 2 should you need it.

But you can import FS1 into it, so you can play both games using the FSO improvements.