Discounting the four seasons of the spin-off series Torchwood, the Torchwood Institute appears in one form or another in the Season 2 episodes "Army of Ghosts" and "Doomsday", and again in Season 4's "The Stolen Earth" and "Journey's End". Jack Harkness (after becoming head of the T.I.) appeared in the Season 3 trilogy "Utopia", "The Sound of Drums" and "Last of the Time Lords", with dialogue references made to the status of his Torchwood team. Finally, the origin of Torchwood is detailed in Season 2's "Tooth and Claw". Aside from this, one-off and unexplained references to Torchwood were made in a number of Season 2 episodes as well as the Season 1 episode "Bad Wolf" as a build up to the big reveal at the end of Season 2, plus a brief after-the-fact reference in "The Runaway Bride".
This just covers the TV show and doesn't include crossovers/references in the novels and comics (IDW published at least one comic story in which the Doctor interacts with members of Torchwood in the 19th century).