Many links below the cut...
First a collection of YouTube links...
farmergeddon71 has produced some very funny videos, making full use of the power of modern computers
Flight of the Darned
The Five Doctors Pt. 1
The Five Doctors Pt. 2
Babelcolour also does fabulous work, though in a more serious vein... Do yourself a favour and at least check out the Time War Trailer.
Classic Doctor Who Tribute: EVERY SINGLE STORY
Doctor Who Trailer: THE TIME WAR
Babelcolour Tribute: THE MASTER
This one did the rounds a while back, but is worth a look if you missed it.
The Steampunk Dalek animation. And if you want to see the original sketch it was based off, visit Promus Kaa's Deviant Art site, for that and some other steampunk Doctor Who goodness.
This also did the rounds, but is quite funny - The Fast-Forwarded bits of the Doctor's Messages to Martha from Human Nature
Now to non-video stuff...
For the knitters out there is EXTERMIKNIT!
The Horror of Fang Rock as told by the Beyeux Tapestry
A short animation showing how daleks used to climb stairs
The Dalek Song
The Tragical History Tour is still my favourite site for pictures from the series. It's been running for ten years and is a great resource. Yes, the official BBC site sometimes has better quality pictures at bigger sizes, but they don't have anywhere near the same range.
The Ten Doctors Comic Archive. I'm way behind with this but what I saw originally I quite enjoyed. May try to catch up later today.
And the best 'til last...Tom Baker Says. Do yourself a favour, go to the Tom Bakaraoke section and check out "Video Killed the Radio Star."
And that done, now I'm off to post some Doctor Who toys to people :)