First, the novelization Halycon just arrived. I want to read it NOW, but... I shall force myself to save it for lunch hour. Yes, boring lunch hour.
Secondly, reading some great stories online, and I recommend Shep whumpers, etc. to check 'em out. They're all still be posted but I can't resist reading them piece by piece.
Deus Ex Machina - http://www.fanfiction.net/s/3118744/1/ by B7Kerravon - a nice post-"Trinity" story of stress, tension and two scientists and a colonel stuck in a haunted lighthouse. Nothing can go wrong, right? Heh!
Honor Bound - http://www.fanfiction.net/s/3117307/1/ by Baroqy - Sheppard goes missing for two weeks and comes back, and he wasn't at a day spa. Angst, Shep whump. Good team interaction.
At What Cost - http://www.fanfiction.net/s/3084032/1/ - Caught in the middle of a bloody civil war, Sheppard and Beckett become separated from the rest of the offworld team. When a rescue team returns, only Sheppard is found. Ronon takes it upon himself to remain behind and search for the physician. Now, I'm not into Beckett whump, but I find the storyline and characterization quite appealing (and oh yeah, Shep did get whumped).
World of Hurt - Consequences - http://www.fanfiction.net/s/3128070/1/ - A "Common Ground" (spoilers) tag that just started. I swore I would stay awau from all CG tags till I finished mine - which frankly, is nothing more than a compilation of scribbled shorthand, so I broke. Quite good!
And well, I've got other stories I recommend but these are the ones I just checked on today. :)