We were there in July. The Sunderland at Hendon was FINALLY open in it's new digs. Outstanding display.
The Churchill War rooms have added the Churchill Museum. We spent about 4 hours in the museum and didn't realize we were there that long.
There's also an interesting little WWII museum on the other side of Tower Bridge from the Tower of London. Has an incredible amount of WWII memorabilia. Some military stuff but mostly stuff from the lives of everyday people. Here's the website:
http://www.britainatwar.co.uk/It's near the London Bridge tube (English for subway

) station but we just walked across London Bridge from the Tower.
I second the suggestion for the Science Museum. It's pretty dark in the a/c section so if you're taking pictures, either take a tripod, for timed photos, or make sure your batteries are fresh for your flash. A wide angle (10-22mm) lens would also be a good ides as things are kinda' on top of each other and you can't back up far enough to get an entire airplane in the photo.
That's all I can think of at this time.
Mudge the hopefully helpful

ps.. Been to Duxford? It's a trip but well worth it. You
could go up and back in a day for about $90 including entry to Duxford. I'll be glad to give you some more specific info if you send me a PM. Train times and such.
pps...Thanks for the reminder fearless. Yes...the HMS Belfast is a must. It's on the same side of the Thames as the little museum I pointed out. You could do both in about 3 hours and they're within walking distance of each other.