1. Han shot first
Wait, wrong canon. In my canon:
1. The Virgin books happened, except for the crap ones. And except for the Looms, which are a rumour spread by elderly Time Lords who don't like to think that sort of thing goes on. Instruments of Darkness happened. Don't ask about the other BBC books - I haven't read most of them. The retcon of the destruction of Skaro definitely didn't happen though. The Big Finish audios also happened.
2. Shada happened; Dimensions in Time happened, but only some of it was real; The Curse of Fatal Death happened in an alternate branching reality; The Scream of the Shalka features a future Doctor and will eventually happen. Possibly.
3. After Dragonfire, Mel kicked Glitz off the Nosferatu II, teamed up with Chris Cwej and a bunch of Sloathes and they all sailed the Twelve Galaxies as pirates.
4. The Doctor did not condemn a human to life as a face on a paving stone, because that would be cruel.
5. The Doctor probably shagged Romana. He hasn't shagged any of his other companions because Time Lord mating is hideously complex and has to be learned in a special course at the Academy. The Rani was his lab partner.
6. The Doctor only had one heart in his first incarnation, because he's half-human. It's a long story.
7. The Eighties-era Cybermen which you can kill by sneezing on them are a crap offshoot. The real Cybermen were still around that whole time, but they were... somewhere else.
8. The chameleon circuit isn't stuck - the TARDIS just likes being a police box. It also likes landing in exciting places and will change course if it sees something interesting.
9. The Eighth Doctor died as a result of the Time War. Other Time Lords survived it, but are all avoiding the Doctor because they're annoyed at him for blowing up their planet. A bunch of them have set up shop on a planet in E-Space.
10. I can't think of anything else, sorry.