Although the TARDIS is technically a time machine, for most episodes the Doctor could rock up in a bus and it wouldn't change anything.
The most obvious answer for me is Blink, with the conversation on the DVD Easter egg. Very cool use of time travel, and seeing it come together is brilliant.
I'll also add Waters of Mars. It's not really got any time travel in, but I feel like the foreknowledge which shapes the plot just about counts.
Dr Who doesn't have that many eps that jump between time in the ep itself so it is a little hard.
I like the Christopher Eccleston run because you see The Doctor have to witness the effects of his actions with the space station.
He also took Rose back to see her dad. She goofed, they went back again, saved him, caused a paradox, and he died anyway to put it all back.
Not the worst episode ever.