May be a little further up Borough High St but I rate the Gladstone. Also second The Rose on Snowfields, The Royal Oak for Sunday lunch, The Rake for beer and a little further east from Tower Br, The Angel (I think it's called that) Samual Smith's pub - fantastic views of the river and cheap prices.
If you are on the Cut I would steer clear of the Windmill - I find the people in there very agressive. A nice meal can be had at Anchor and Hope (corner of the Cut and Hatfields) but you'll need to turn up early (ie before 6pm) to get a table as they don't take reservations
I think the The Rake is massively overrated - great for a wide selection of bottled beer but if you like it on cask they only seem to get one barrell of each beer in and then rotate it to the next beer. Just as you find one that you like it's gone!
Plus it has the worst pub toilets I've seen. And I've been to a few pubs...
Far better in my opiion are the Market Porter, the Woolpack and The Bridge House on Tower Bridge. The three Davy's pubs on Tooley Street are all good too.
There are loads of pubs in SE1, but many are full of passing trade and/or tourists and hence lack most of the feel of a proper boozer.
The George on Borough High Street and The Anchor at Bankside are perfect examples of historic pubs that feel, IMHO, Hollywoodized. You can almost see Dick Van Dyke sitting in the corner!!
But you should not settle for this as SE1 has some of the best pubs left in London. As in most places your better off moving slightly off the beaten track to get the real thing, and there's lots of that in and around the area. Search on Beer in the Evening (http://www.beerintheevening.com/) for SE1, Southwark, Bermondsey, London Bridge, and you'll get hundreds of choices.
Personally, I second the nominations so far for The Royal Oak on Tabard Street (the only Harveys pub in London) and Lord Clyde on Clenham Street, apparently the shortest street (not Close, Walk or Place) in London. Both I would class as pubs for drinking, with the RO being a little swankier, and with the option of food. All the pubs on the upper part of Bermondsey Street do food and have a younger, though not infantile clientele, especially on the weekends. The Marigold on the lower part of Bermondsey Street is my local and a particular favourite. Local pub. I also really like the Rose & Crown on Colombo Street, which sometimes gets the better of me as I come out the gym across the road. Also nobody's mentioned The Old School Yard on Long Lane, fantastic for a night out partying (which I will hopefully be doing later) with excellent cocktails. And finally really off the track for passing trade and tourists is The Victoria on Pages Walk. One of my favourite pubs in the area, but it may be an acquired taste. I brought people from work here. Half loved it, and the other half spent the whole evening worrying if they were gonna get battered or not (sheltered upbringing I think!), which of course was never on the cards.
Whatever find a nice pub that suits you guys, enjoy a good pint and wonder what it would be like if you lived in the best part of the best city on Earth, and could visit regularly.
No connection to any pub mentioned, or BITE, save as a punter.
Thanks for all the recommendations :-) My in-laws will be impressed of my SE1 Pub skills!! BTW, the City doesn´t close during Easter, does it? We´re in London April 11th-14th
Thanks again //Patrik, Stockholm Sweden
As stated though don't be tempted to eat there and to underline that it is extremely expensive for often unfriendly service. The Lord Clyde is my local and looks the part of a traditional english pub. On a personal note as it's been mentioned, can I ask why the Marigold is so quiet on a Friday night? I took some friends there a couple of weeks back and we had a great time playing Kerplunk in a very cosy atmosphere with a bar virtually empty apart from about six locals and with generous opening hours.