Here's some thoughts on what works for me, my moods and my overall response.
For the love of downbeat:
Turn Left - bleak, and even bleaker in the light of what comes afterwards for Donna. And Bad Wolf.
For the tears:
Journey's End - oh come on, whatever faults it has - and I know there are many - the horror of what happens to Donna and Wilf's final scenes are just pure tear-fests
Father's Day - because damn it may be cheesy but it works
Doomsday - yes, I know some of you will think it's a contradiction to praise both JE and D in the same breath, but regardless of HandDoctor and the beach revisitation I still well up at the ending of Rose and the Doctor (even though the balance of the episode overall is skewed)
For the fan-girl in me:
Utopia - I refer you to the Squeeing...
School Reunion - Sarah Jane!!!
Time-Crash - grinning pretty much throughout
For the needing of daylight to watch them:
Blink - freaky blooming Moff.
The Empty Child/The Doctor Dances - freaky blooming Moff!
Midnight - don't you dare repeat my words
For the punching the air:
The Christmas Invasion - come on, when the Doctor comes out of the TARDIS, it was a great moment.
Tooth and Claw - for the Doctor putting on his glasses
The Family of Blood - "you really shouldn't have let me press all those buttons"
For the story-telling:
The Unquiet Dead - a gloriously put together spooky narrative
The Girl in the Fireplace - for with and tears and scares and love
Dalek - the best of the Nu-Who dalek tales
So what do I do now? I'm tempted to try and be even-handed. But I don't think it can work with just three to choose.
- Human Nature/Family of Blood - because it makes me tingle beautifully
- The Girl in the Fireplace - because you can't always get what you want (but the pay-off of the final shot just rounds this story so well)
- Turn Left - because Donna just plays a blinder and although the Doctor is only in it briefly his playing of the scene when Donna edges towards saying who she saw is breathtaking.
Not original choices I grant you, but there you go.
Honourable mentions for: The Christmas Invasion, Utopia/Sound of Drums, Blink... oh and everything from Silence in the Library/Forest of the Dead up until the white heaven saved ending... and... and... and...
Oh crap. I could come up with justification for almost any episode (fill in your own most unfavourite here no doubt).