Advantage - by Resonant, Aliens turn John into Rodney's slave.
Now I usually don't like slave fics along the same lines for why don't like BDSM fics the characters are usually way OOC and I'm also not much for dark fics unless I am absolutely sure that there will be a happy ending. This is not like any slave fic I've gritted my teeth through, it's actually really funny, John gets turned into Rodney's slave, but he is possibly the most cheerful and bossy slave I've read about. Rodney is of course reluctant but hey if your going to have a slave following you around demanding you make him do things why not let him make you, make him right? There is also juggling and very cute scenes of John taking care of Rodney in his sarcastic, shut-up-Rodney kinda way.
A Beautiful Lifetime Event - by Shallot, John and Rodney have a baby thanks to ancient technology, and it of course changes their lives.
Shallot has alot of really great SGA fics but this one is by far my favorite. I'm not sure why I like to read about John and Rodney as dad's but I really really do, fills me with wooby feelings and happy family fantasies. Their relationship builds slowly or as John puts it "I didn't know I was already married" and the sex isn't till the end but it's worth the wait as it is all the more satisfying. I absolutely love their daughter in this fic, but I got to love any girl who wants a power drill set and a hot pink Barbie car.
The Chair- by Xanthe, Rodney is genetically destined for John....this is not as great as it sounds.
This is Xanthe's first ever SGA fic and you can tell as the voices are alittle rough to me but even then the story is still awesome. Rodney discovers that there is another chair and that it can harness energy to use as a powerful weapon. What kind of power does it run one you ask? Well seeing as how this is a slash fic it uses human sexual energy and that's where John and Rodney jump in. John is the only one who can use the chair because of the ATA gene and Rodney is his genetic match. Now I would consider this the definition of the "fuck or die" story.