I agree - TCI was magnificent, as was School Reunion. Not only Sarah Jane and K-9, but evil!Krillitane!Giles as well! And Time Crash! "You were MY Doctor." *squee*
Boom Town only had two purposes, as far as I can see:
1. Show the ending of Rose's relationship with Mickey, thus setting up his departure;
2. Make sure everyone can pronounce Raxacoricofallopatorius.
Although the scene in the alley beside the mayor's office where Margaret the Slitheen keeps transmatting away only to be brought right back again is pretty hilarous.
As much as Doomsday just crushed me, I'd have to say it was a brilliant ep.
As far as S3 and Martha goes, I think Blink is my favorite ep - though it's rather Doctor-lite - and Human Nature/FOB was the best story, even if I did cringe for poor Martha. Like it wasn't enough that she had to live with Rose's ghost every day, but to shove Joan Redfern in her face?