5. John Smith
John Smith is actually the Doctor himself. In order to protect himself and his companion at the time, Martha Jones, the Doctor erases his memories (temporarily) to sort of camouflage himself as a human. He ends up as a professor at an all boys school right before WWI. Martha is his maid, and he ends up falling in love with the head nurse. The aliens that they're hiding from obviously find him and everything gets all kind of messed up. The Doctor's memories are preserved in this pocket watch that a young school boy finds and eventually (after almost two entire episodes) gives back to the doctor. The following is the heartbreaking scene when the Doctor has to decide if he stays John Smith the innocent human school teacher or the Doctor.
4. Donna Nobel
I really personally wanted to put this higher in the list. But I know Donna's not everyone's favorite (despite that she's my number 1 girl for life). Through chance, fate, luck, or whatever, Donna ends up being THE most important person in the universe. At the end of her only season, she manages to save the entire universe by crossing her DNA with the Doctor's. While it gives her the brains of a TimeLord and the creativity of a human, the TimeLord DNA is slowly killing her. The only way the Doctor can save his absolute best friend is to erase of trace of TimeLord from her system, including her memories.
3. Rose Tyler
Okay, to be absolutely honest, it really is a toss up between Rose and Amy for this 3/2 spot. But I'll stick with Rose as number 3, because I don't think there was as much of an emotional impact with her. I mean of course there was at the time, but my Amy Pond wounds are still healing.
Anyway, Rose and the Doctor come home to find that the world has been invaded by two different alien species who don't like each other and who really want to take over the human race. In order to save the world (again), the Doctor opens up this like, portal thing and sends all the aliens into a black hole so to speak. But it only works by picking up on particles from outer space. So, while it does suck up every little alien, it also really really really wants Rose and the Doctor (because as they're outer space travelers, they're covered in particles). Bracing themselves as best they could, Rose manages to lose her grip and begins to get sucked in. But her father (sort of), grabs her and sucks her into a parallel world. Here is the absolutely devestating goodbye scene
This still kills me. I'm going through some serious TV heartbreak here kids. Okay, so Amy, her husband Rory, and the Doctor are hanging out in NYC. They're reading this book (which later turns out to be a map of events for them), and notice Rory disappears. A Weeping Angel (google it) took him to the 1920's. Amy and the Doctor dutifully go to get him. It's there we discover the Angels plan. They grab humans and put them back in time and feed of the crazy time energy that results from travelling like that. Rory ends up watching an 80 some year old version of himself die. But no the Doctor's totally going to save them and it'll be fine right? Yeah, totally.
So Rory gets this crazy idea to jump off the building, the idea being that if he dies twice in one day, a big enough paradox would be created that the Weeping Angels would die. It's nowhere on youtube, but let me tell you, the scene when Amy and Rory hold onto each other as they jump off the roof is utterly gut-wrenching. I had big fat tears rolling down my cheeks thinking "Oh god this is it! NO!!"
But there's a big bright light and they're fine. Everyone's fine. And it's only when Rory notices his name on a tombstone that one surviving Angel grabs him and sends him back in time. The Doctor is in tears begging Amy to stay, to try and move on, to not go after him. But Amy can't. She walks into the arms of this Angel and joins her husband, and the tombstone changes to add her name and their ages when they died.
Here's a fanmade video that sort of sums things up
Some of you might know this, but most don't--the Doctor can "regenerate". They give this whole thing about how when his body is damaged enough it will regenerate into an entirely new body--but really, it's just a clever plot device to switch out actors whenever they want.
The episode when the 10th Doctor regenerates into the 11th is probably the worst for me. It absolutely destroys me every single time I watch it. There was even a special song written for it, an aria written in Latin called "Vale Decem" which means "Farewell Ten". ARE WE KIDDING?!?!?
Anyway, the final episode is all about fighting off his enemy, The Master. He recruits his old friend Donna's grandpop (Wilfred) to help and at the end of the day when the fighting is done, Wilfred is trapped in a radioactive chamber, that he can only be released from if someone opens the opposite door and takes his place. The Doctor, after one of the most impressive Who monologues ever, pushes the button, releases Wilfred, and absorbs all the radiation. And as his body slowly dies, he takes the time to silently go through time and say goodbye to all of his former companions, the last being the one he truly truly loved--Rose Tyler.