While its not exactly marking tracks within a single WAV, you may be able to hit FF (if you can make new track without any loss) and make your tracks that way.
Once, when I was taping Ween, I was getting close to the 2hr. limit on the JB3. Rather than have it cut over to the new track in the middle of a song, I hit FF and started a new track for that last few songs. Basically, I made a CD cut. Later when I used CDWave, I kept that particular cut, since it was at the end of the encore break...
The JB3 didn't mark tracks, but you could hit FF at any point and pretty much do the same thing... I don't own the JB3 anymore, I use an HDP2 now, but I bet you could do something similar with almost any deck.
Terry