Some of these are John/Rodney oriented, some Jack/Daniel, some both, but all are Daniel on Atlantis:

dk_valentine's Company (http://dk-valentine.livejournal.com/194187.html) John/Rodney, Jack/Daniel

ethrosdemon's Once Upon a Time (http://ethrosdemon.livejournal.com/310178.html) John/Rodney

findo's Five ways Daniel improves Atlantis. (http://findo.livejournal.com/3333.html) Jack/Daniel, John/Rodney.

icarusancalion's Colony Atlantis (http://www.icarus.slashcity.net/stories/colonyatlantis.html) Jack/Daniel

ladyra's Wraith Killers (http://www.wraithbait.com/viewstory.php?sid=12387&warning=12) John/Rodney, Jack/Daniel

nixa_jane and ForCryinOutLoud's Brave New World (http://community.livejournal.com/mckay_sheppard/1732968.html) John/Rodney, Jack/Daniel.

nixa_jane's Geniuses (http://community.livejournal.com/nixa_jane/4966.html) John/Rodney, Jack/Daniel

saffronhouse's Entangled (http://saffronhouse.livejournal.com/97031.html) Jack/Daniel

theemdash's Bickering (http://what-works.livejournal.com/16276.html) Jack/Daniel, John/Rodney

xela_fic's The Daniel and Rodney Snark Fest of Pornographic Doom (http://community.livejournal.com/sga_santa/159325.html) John/Rodney, Jack/Daniel, various.