Right, second half of my top ten favourites (and eagle-eyed readers will note I'm going in chronological order because I too, am using my boxset running orders to work it out...)
Smith and Jones. Ten and Martha, third series. I included this instead of Blink, actually, because I really loved the Martha that was introduced in this story. She flirted (and was flirted with by the Doctor), but she was also clever, brave and not afraid to good-naturedly mock him. If she'd have been written like that for the rest of the series, it would have been much better, but she got lumbered with the crush storyline, and some truly dire scripts (Dalek Cabaret, I'm looking at you)
Human Nature/Family of Blood, Ten and Martha. As already mentioned, the scarecrow episodes where he becomes human. An astonishingly good performance from Tennant, particularly the bit where he switches instantly from the Doctor's voice to John Smith's. Martha also shines, I love the bit just before she slaps him.
Utopia, Ten, Martha and Jack for all the reasons serenity mentioned (Jack/Ten flirting, muchly yes) but primarily for Chan Tho and Derek Jacobi's all-too-short stint. Could have watched him for ages.
Fires of Pompeii, Ten and Donna. Just the right pitch of funny (The Welsh running gag!) and moving, and plenty of spine-tingling moment of foreshadowing (more than we realized in hindsight, of course - Donna and the Doctor pressing the plunger togther etc.)
Silence in the Library/Forest of the Dead, Ten, Donna, River Song. Loved the atmosphere, again, and the mystery romance stuff. Wasn't 100% on the very end, but the rest of it was so good, I forgive a little bit of cheating to get rid of the monster.