IMHO the British Museum is well worth seeing. 200 years of plundering antiquities from ancient civilizations has its perks, lots of interesting Assyrian, Egyptian and Greek stuff.
Otherwise I'd recommend the National Gallery if you're at all interested in art, and the Imperial War Museum. The former is on Trafalgar Square so has the advantage that you can just pop in while wandering around the main tourist bits, the latter however is out in the middle of nowhere on the south bank of the river and is quite a trip to reach.
The above three all have the added bonus that, last time I checked, they were all free admission (as I believe are most if not all the major museums in London).
Otherwise the Tate Modern has two reasons to visit:
1) The building itself (a former power station) is pretty impressive on the inside.
2) The cafe at the top is quite nice (and you can skip straight past the modern art to the top if you want).
Also, it's a nice walk from there along the river bank to parliament square, from which you can then easily get to Trafalgar Square via Pall Mall, thus seeing half the "famous" bits of London in one fell swoop.
The Science Museum and the Natural History museum are OK, though a little too "kiddy-friendly" for my tastes (though I do work in science, so a historian may well say the same thing about the British Museum).
I haven't been to the Tower in years, but IIRC it was expensive and crowded, though quite fun if you fancy something a bit less serious after all the highbrow art and ancient history.
Avoid the Underground at rush hour (though I suppose that applies to any major city), and I would recommend getting an Oyster card when you first use it, it's not any cheaper but makes getting the Tube a whole lot easier. Try not to have a heart attack when you see how much it costs for a cup of coffee anywhere in London. Be prepared to be molested and have your bag searched (and very likely be glared at by panicky-looking policemen with submachine guns) every time you enter anywhere.
I'm not quite sure why London seems so unpopular here, IMHO of the major cities I've visited London is as good as any, and a lot better than most. Certainly I can't think of anywhere where you can find as much interesting stuff to do for free.
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