Dear lord, this thread might be the one that actually cures me of missing London! (You'd have to work very hard to make me prefer The Town That Time Forgot, though.) I left in 2005 and haven't even been there since 2007.
Stockpot, BlueNote, ALL the pubs you've mentioned (
), fascinating shops run by fascinating people. The Marquee, anyone? Also upstairs at Ronnie Scott's, Jimmy the Greek's and numerous unmarked drinking/gambling dives that were cheap & open all night, often above Chinese restaurants in Soho or in basements under offices.
I was very lucky; I worked in Soho, Fitzroviaaahh before it was called that, in Covent Garden and Clerkenwell. Then in Canary Wharf, after which life started going downhill. XH1 and I had a big row because we nearly bought a house in Fitzroviaaahh - it was cheap
- but he wanted the bijou cottage in Wandsworth, which we bought. Argh.
What was that massive second hand shop on Long Acre? - American Retro :) I also used to buy Forces surplus gear from an odd shop near Mornington Crescent, but that was 80s I think. Fifty - Home was wanktastic, but felt a bit special because it was one of the first "pretend this is someone's house, but really it's a snooty club where everyone's done too much coke" places 
Centrale & all the other lovely cheap restaurants. Up All Night and Crazy Larry's - noddy, I've often wondered if we knew each other in a previous life, and I think we must have!
Ohhh, THANK YOU for this thread OP
I'm feeling all bathed in the golden glow of nostalgia and feeling other people get it.