This meme is evil. How am I supposed to choose three?
1. SGA/Eureka series by rageprufrock Summer House / Shore Leave / Sabbatical - HILARIOUS. It's so interesting to read about John and Rodney on vacation from someone else's point of view, and everyone's various reactions to Rodney's arrival in town, to Rodney's status as totally whipped. This fic makes you realize that John and Rodney would totally fit in if they lived in Eureka - they're the right kind of crazy. I think readers should be able to understand this even without having seen Eureka. In fact, these fics are what made me want to watch Eureka.
2. A Farm in Iowa by sheafrotherdon- I really, really love this series. I have a fondness for kid!fic, but the problem is that I have to like the kid. Finn McKay is absolutely adorable, a joy to read. This fic has made me laugh, made me cry, and gave me this wonderful sense of satisfaction when I finish it. I always feel like I'm saying goodbye to a dear friend when I finish this. If you're going to read an AU series, you should read this one.
3. BDSM Universe xanthe - If you've known me for some time, you've heard me talk about my preference for sub!Rodney, which goes against fandom-wide preference, it seems. I don't mind sub!John, and I'm working on liking it more (by giving it a second chance - (my new years resolution) - instead of immediately hitting the back button), but I just find sub!Rodney hotter. This series delivers. xanthe posits a simple question: What if the norm was being bisexual and into BDSM? How would that change things? Different experiences shape the characters into different, but still recognizable people. And then they meet "our" John and Rodney. IDK, I just love it.