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.
"A Christmas Carol" springs to mind as one of my favorites with in-episode time travel. What's more Doctor than trying to save the day by retroactively making the villain your friend?
“Vincent and The Doctor,” when the Doctor takes Vincent to the Musée d'Orsay. I love how the background music starts as diegetic, playing from a boombox, then you have a wide-eyed Van Gogh taking in all of the exhibits. I’d love to be able to tour a museum like that with a master of the craft. It culminates with Bill Nighy’s curator character giving a glowing description of Van Gogh’s body of work with the man himself standing right behind him, and it’s time to turn on the waterworks.