The mcgann/capaldi handover mini episodes canonises elements (at least) of the audio plays (charlie and crizz mentioned by name), which is problematic because the 2005+ series borrows liberally from "Jubilee" and more recently "The Steel Turk" (sorry gaiman fans, he didnt even come up with the coolest thing in that episode).

in sutekh land the 63-89 run is canon but the TVM and 2005+ are set in different universes (respectively, tvm has its own because of the half human doctor).

the audio plays, 90s new adventure and BBC eighth doctor books also take place in alt universes.

This way everything counts and yet sort of doesn't... Inter dimensional incestuousness provides neat explanations for the way dead doctors can turn up and yet look older than they did when they died

i'll stop talking before i betray my cool exterior