I'm certainly no expert, nor did I pop onto NADA or KBB, but if the bike seems to run/shift fine, I would think it is worth it. Is the chain shot, or could a couple of links be removed? Is the sprocket worn? I would take a close look at the forks and shock to see if there is any evidence of leaks. Check some other simple things such as brake pads, brake lines, close examination of the motor after it has run awhile to see if there are any leaks, etc. Heck, my g/f just traded in her 03 Bandit 600S with 18,000 miles, a couple/few scuffs (from soft luggage), and a dimpled tank for $2500. And no, the bike she bought wasn't marked up...actually, it was on sale. An '06 SV-650S for $4995. Sweet!!

Good luck...
Cheers,
Joe