We recently encountered a student bassoon that had an extremely bad case of rot in the boot joint. Here are some pictures of the affected area when we received the instrument and after our repair tech Matt was done with replacing the rotted section of the boot and cleaning up the bracket. The bore has been lacquered, so it reflects the light in unusual ways. There is also some sealing wax visible around the area. You can see the line where the new wood meets the old all the way past the G tone hole (the one that is closed when you depress the F key)! Nearly 5 inches of the bore was replaced.
Rot like this is caused by consistently resting the bassoon across the lap of the player when not playing, and by not swabbing the instrument out after every session. Moisture settles into the wood, and over time causes the wood to swell, crack, and even grow moldy! Always swab your instrument after every use, and don't lay the instrument down sideways in any way during rehearsals or practice.
More photos can be seen in this album on our Google+ page.