We stuck to the West End so didn't get to all the pubs mentioned above, but of those we did drink in:
The Hanging Bat is fantastic, with an expected upgrade to stunning once the beer from the onsite nanobrewery is available. My other favourite from the weekend was the Caley Sample Room -- a bit out of the way but easily got to by bus, and probably worth it.
I loved The Cloisters but The Red Squirrel was a disappointment: no cask, very few of the keg fonts had beer, and the one I tasted wasn't very good. Maybe we caught it on a bad day. It's a short hop from The Hanging Bat and close to loads of other West End pubs, so it's not a big investment to have a look in.
Regarding traditional pubs, there was a great selection in The Blue Blazer and Thomson's was also good. Both are among just four pubs in Edinburgh (a local told me) which serve beer by the "tall font" Scottish air pressure method. Real Ale with extraneous gas: quite a rarity <!-- s:) --><img src="{SMILIES_PATH}/icon_smile.gif" alt="

" title="Smile" /><!-- s:) --> The Bow Bar is another of the four but I can't remember the other one.