I know that FSO on Linux (and probably OSX as well) supports having mods folders in different places (like either the main freespace2 directory, or ~/.fs2_open, and possibly a 3rd place) but I don't know about Windows (sorry).
If you have Windows Vista or newer, you can use mklink command to create either symbolic links or junction points. Practically they're pretty much identical in how they function to the end-user. However, in some rare cases junction points have proved to work more reliably with some software.
Windows XP does not have built-in command to create junction points and XP does not support symbolic links. There is however a tool called Junction to create junction points.http://technet.microsoft.com/en-us/sysinternals/bb896768.aspx
So, what can I accomplish with mklink or Junction tool? For example, you have FS2 installed to C:\Games\FreeSpace2. You can install Blue Planet to D:\FS2mods\blueplanet, then create junction point (or symbolic link) to C:\Games\FreeSpace2\blueplanet and have it point to D:\FS2mods\blueplanet. Then as far as FS2 is concerned, the mod is installed in C:\Games\FreeSpace2\blueplanet.
Windows Vista, 7 and 8 use junction points to provide backwards compatibility for applications that were designed for XP or 2000.
Mklink is very useful especially to SSD owners who can move their applications and games to and from SSD without having to reinstall them.