2005
(8th Doctor, EDA) Genocide, by Paul Leonard
(8th Doctor, NA) The Dying Days, by Lance Parkin
2006
(1st Doctor, nov) Doctor Who - The Reign of Terror, by Ian Marter
(1st Doctor, nov) Doctor Who - The Rescue, by Ian Marter
(2nd Doctor, nov) Doctor Who and the Enemy of the World, by Ian Marter
(2nd Doctor, nov) Doctor Who - The Dominators, by Ian Marter
(2nd Doctor, nov) Doctor Who - The Invasion, by Ian Marter
(4th Doctor, nov) Doctor Who and the Ark in Space, by Ian Marter
(4th Doctor, nov) Doctor Who and the Sontaran Experiment, by Ian Marter
(4th Doctor, MA) Evolution, by John Peel
(4th Doctor, nov) Doctor Who and the Ribos Operation, by Ian Marter
(5th Doctor, nov) Doctor Who - Earthshock, by Ian Marter
(9th Doctor, NSA) The Clockwise Man, by Justin Richards
(9th Doctor, NSA) The Monsters Inside, by Stephen Cole
(9th Doctor, NSA) The Stealers of Dreams, by Steve Lyons
(Companions) Harry Sullivan's War, by Ian Marter
2008
(1st Doctor, annual) The Doctor Who Annual 1966
(7th Doctor, NA) Theatre of War, by Justin Richards
(8th Doctor, EDA) Interference II, by Laurence Miles
(unofficial) Campaign, by Jim Mortimore
2009
(1st Doctor, script) Farewell Great Macedon, by Moris Farhi
(6th Doctor, MA) Time Of Your Life, by Steve Lyons
(6th Doctor, MA) Millennial Rites, by Craig Hinton
(6th Doctor, PDA) Spiral Scratch, by Gary Russell
(Bernice Summerfield) Beyond The Sun, by Matthew Jones
(Torchwood) Border Princes, by Dan Abnett
2010
(4th and 8th Doctors, PDA) Wolfsbane, by Jacqueline Rayner
(4th Doctor, annual) The Doctor Who Annual 1976
(4th Doctor, MA) System Shock, by Justin Richards
(4th Doctor, annual) Doctor Who Annual 1977
(7th Doctor, NA) Lucifer Rising, by Andy Lane and Jim Mortimore
(7th Doctor, NA) White Darkness, by David McIntee
(8th Doctor, EDA) Placebo Effect, by Gary Russell
(11th Doctor, NSA) The Coming of the Terraphiles, by Michael Moorcock
2011
(2nd Doctor, PDA) Dreams of Empire, by Justin Richards
(2nd Doctor, script) The Prison In Space, by Dick Sharples, ed. Richard Bignell
(8th Doctor, EDA) Autumn Mist, by David A. McIntee
(11th Doctor, double) Heart of Stone, by Trevor Baxendale / Death Riders, by Justin Richards
(Torchwood) Pack Animals, by Peter Anghelides
My personal top five from the above list, in the order that I read them:
Doctor Who - The Rescue is the best of Ian Marter's ten Who novelisations and one of the best novelisations full stop. He takes a fairly slight two-part story which was basically a vehicle to introduce a new regular character, and invests it with vastly more detail and context, to make a particularly satisfying read for the range. It was the last book he finished before his death.
Farewell, Great Macedon is an extraordinary story that was never made, which would have brought the original Tardis crew to the deathbed of Alexander the Great. The book also includes a one-episode story of an alien who dies for love of Barbara. Big Finish recently did a decent audio adaptation of both, but the script book has lots of interesting detail.
I've only read two Bernice Summerfield novels, and one of those was before I started bookblogging, so Beyond The Sun stands as an enticement to an entire range of Who books of which I know very little. It's an excellent yarn of alien threat and psychological differences among a small team, perhaps consciously modelled on Colony in Space but an awful lot better.
The Torchwood novels in general were very good; Border Princes was the first I actually read rather than listening to, and I found it a witty and clever reflection on the first season - taking the plot of the Buffy episode Superstar and transferring it to Cardiff.
Finally, to actually include a novel from one of the major runs, I much enjoyed Dreams of Empire which takes the Second Doctor and team to what appears to be the last fortress of a dying Roman-style imperium, though of course it turns out that there is a lot more going on; intricately and engagingly plotted.
Honourable mentions:
The Dying Days, by Lance Parkin
Evolution, by John Peel
The Doctor Who Annual 1966
Campaign, by Jim Mortimore
The Coming of the Terraphiles, by Michael Moorcock
One to skip - the story we should be glad was never made - the misogynistic Prison in Space.