This was lovely, and I completely agree with dark_aegis above about the emotions coming through very strongly. Also second the rec that wendymr made for Fayhe's "Suture" (and everyone else's recs as well).

Since everyone's doing recs I might as well jump in as well :)

FUZZY by wired_lizard (Jack/Rose, 9) - NC-17 for smut - This one's more Jack/Rose, but their "interaction" (ahem!) has everything to do with the Doctor, plus a really original take on telepathy. This is also supposed to be a prequel for 9/Rose/Jack story still to be written (hopefully she'll write it).
http://community.livejournal.com/dwfiction/479682.html

HANA-MI by aervir (9/Rose/Jack) - PG-13 - The cherry blossoms are in bloom in Japan; lovely little slice of life (takes place between "Boomtown" and "Bad Wolf")
http://community.livejournal.com/time_and_chips/1431182.html

"Something Like Moebius" by doyle_sb4 - G - The author's summary is best: Eleven-year-old Jack has your typical possessed-alien-teacher experience (also contains an adult Jack, Rose and the Doctor- not OT3 in the strictest sense, but who can resist eleven-year old Jack?)
http://doyle-sb4.livejournal.com/390405.html

"They Danced" by taleya - NC-17 - 9/Rose/Jack smut - hot! Mostly PWP, but it's very well written. This one's a classic:
http://homepages.ihug.com.au/~taleya/dw/dance.html

"Slightly Psychic Confessions" by Casira - NC-17 - 9/Rose/Jack - Another incredibly hot PWP that makes very original use of psychic paper. Another early classic!
http://www.whofic.com/viewstory.php?sid=3273&warning=NC-17

"Acceptance and Loss" by ponygirl72 - PG13 - 9, Rose, Jack friendship - This is another one of those stories that does a wonderful job of showing the growing friendship between Jack, Rose and the Doctor. It's also got an excellent action/adventure plot, and the hospital scene between Jack and the Doctor just kills me every time I read it. Be sure to check out the sequel.
http://www.whofic.com/viewstory.php?sid=5468

ACTS OF NECESSITY by aeshna_uk (Jack/Rose, 9th Doctor) - NC17 - Pretty much a hurt/comfort type of sex story, but really impressive for the excellent characterization of all the principles. Even though the Doctor doesn't get any horizontal action, I loved the characterization of him in this story, where driven by his inner demons, he can't help but hurt those around him.
http://aeshna-uk.livejournal.com/2173.html

FIVE TIMES JACK THOUGHT BETTER OF IT by lightgetsin - (9/Rose/Jack) - PG-13 - Lovely Jack POV observations starting in "The Empty Child" and ending post-Satellite 5.
http://lightgetsin.livejournal.com/241488.html
(also check out other stories by lightgetsin, he/she has also done some really good smutty OT3s as well)

wendymr's done lots of great OT3 stories, but I think this is my favorite one:
FINDING JUDAS by wendymr - (10/Jack, 10/Rose) - Mostly PG-13 but with a couple of very R parts - Probably my favorite reunion fic that proves the old adage that you can't go home again.
http://www.whofic.com/viewstory.php?sid=8907
(be sure to check out the sequels!)