You are just listening for any odd sounding noise, i.e. a whine, grinding, something other than normal mechanical operating sound, or flopping around of the shifter. All you should really hear is just the whir of the transmission and engine noise. With the test drive the shifter shouldn't flop around or pop out of gear either. If it does it could be as simple as replacing the shifter bushings or an indication of needing a rebuild.
As I mentioned above, if there are any issues w/the transmission, I wouldn't walk away from the deal(if you want the truck), you can always use the issues to negotiate a better trade.
