One of my favourites include the Zetland Arms on Old Brompton Road, popular with postgrad students and professors of Imperial College (I am an alumnus). I remember spending many a Friday night there with fellow students. It was especially convenient because home was only 5 minutes away so I had no worries about getting drunk in a strange place and not finding my way back!
A couple of fine pubs I went to recently: Ye Old Mitre and the Cittie of York, both near the Chancery Lane tube station. The former is fascinating in that it is nearly 500 years old! You walk in through a tiny lane and boom! into a one-room establishment with low ceilings and old timberwork. Being in the City and so secluded, it is relatively tourist-free except for the times when the walking tours descend on the place. It is very popular with the local workers, discussing the latest merger or the state of the stock market. The local brews are very good indeed. Because of its meagre size, most punters flow into the surrounding narrow lane. The atmosphere is excellent - it you squint your eyes, you may just be able to visualize the 1500s, the pub awash with highwaymen and smugglers doing shady deals in equally dark corners, drinking pints and laughing raucously.
Being on the main road, the Cittie of York may seem a bit more mainstream, but it is also not on the typical tourist route, and attracts throngs of financial and legal workers from the surroundings. It is deceptively large and also reminiscent of older glory. I love the little booths which give you that much more privacy. Again, nice local brews.
To experience more authentic pubs, try taking a walking tour which takes you on a pub crawl. The London tourist information centre (search online) should have brochures and ideas.
Cittie of York: 22 High Holborn, London, WC1V 6BS Ph: 020 7242 7670
Ye Old Mitre: 1, Ely Court, Ely Place, London, EC1N 6SJ Ph: 020 7405 4751
The Zetland Arms: 2 Bute Street, Kensington, London, SW7 3EX Ph: 020 7589 3813 just 2 mins from South Kensington station.