If you're going to do the Science Museum, the Victoria & Albert, Natural History (remember to look at the mad external architechture), and Geological Museum is right next door.
If you want to do a serious tourist walk (given your short stay), start at The Mall and Buckingham Palace. Go east to Picadilly Circus, walk across Leicester Square, to Covent Garden, then south-west towards Trafalgar Square (National Portrait Gallery, Nelsons Column). Then go south down Whitehall (Admiralty Gate, Horseguards Parade, Downing Street) to the Houses Of Parliament and Westminister Abbey. Then cross Westminister Bridge to the London Eye, and walk north and east along the South Bank. Drop into Tate Modern, then cross the Millennuim Bridge to St Paul's Catherderal. Go north-west towards past the Old Bailey and towards High Holborn, then north towards the British Museum. Then you can go west towards Oxford Street (drop into Forbidden Planet if you are a SF geek), down Oxford Street to Marble Arch, and then to Hyde Park and the Serpentine.
Bear in mind, this is an insane amount of walking, so you may want to jump on buses, but you will miss stuff as there really is load of stuff to see and do in London alone (pick up a copy of Time Out if you want to catch any specific events or shows). It is doable in one day if you are fit and take it easy, but you don't really have the time to look around all these places too much unless you want to split it into more than one long day.
If you fancy a day out of London, Stonehenge and Salisbury Cathedral is an easy day out if you can hire a car for a day.
Kew Gardens or RHS Wisley are also good, but at that time of the year there is not a lot to see as it's not really the best time for gardens.
If you're going to zip around London on public transport, get an Oyster Card. There is a £3 depost on them you can reclaim along with any remaining credit before you leave. You fill Oyster Cards up at tube stations (the machines take cash or credit cards and transfer the credit to the Oyster Card) and then you just wave them over the sensors at tube stations gates or in buses. You can regsiter them online (in case you lose them) and then charge them up at the website with a credit card if you have net access.
If you fancy a stage play, most of the theatres are around Shaftesbury Avenue/Drury Lane.
China Town is just north of Leicester Square.
Regents Park and London Zoo might be worth a visit.
It will be cold, but a tourist boat down the Thames is quite good (can pick one up at the London Eye if you want to).
I don't think Tussauds is really worth the wait unless you're really into waxworks. There's always a massive queue of tourists (I drive past it fairly regularly when I visit my parents).
There's often a queue for the Eye, but it is quite a spectacular view and worth the time. You can climb up to the top of the dome at St Pauls if you're fit to climb a lot of steps and it's all open. Bear in mind there are some scary metal steps right at the top.
but still, what to do when we get there?
