My 1996 5spd Legacy has the same rattle problem. The sound seems to be coming from the first link below the shift knob, so that is what I am going to try to replace first.
The bushings and spacers only cost a couple of bucks. The rattle started about 8 months ago, only in 2nd and 3rd gears, and went away if I would push, pull, or twist the shift lever (gently). Over time, the rattle has moved to the other gear positions, and I am really annoyed by the constant rattle!!
By the way, a mechanic I went to said he was going to replace all the bushings, etc, and that the parts would br around $69 and with labor probably a total of $150.
I hope I can fix it myself without too much hassle.