I don't see the usable aspect for junction points. They are dangerous (at least on XP; doing things with the junction point may/will affect the target content), cannot be created for files, only for folders, cannot be created across volumes, etc. No, I'm an all Windows user, don't know if this holds true for anything but NTFS.
Symlinks on the other hand,
from Vista and up, are very easy. Can be created to files and folders, can be created across volumes, across network, can be deleted without affecting the target content and so on. I use
Link Shell Extension to deal with them (which actually handles Hardlinks, Junctions, Volume Mountpoints and Vista/Win7 Symbolic Links).
My main problems is that I'm gettin' the real, zillion characters long paths instead of the symlinks ones in MC. No idea if this is MC-related, Windows-related, etc.