Gunslinger Girl is the next show to go the way of tacking on video only episodes to the DVD release. (Via Anime News Network).
Two additional episodes will be offered on the DVDs for Gunslinger Girl - Il Teatrino (the sequel to the original Gunslinger Girl anime, which was distributed domestically by FUNimation, who also have the rights to the sequel) - "Light of Vanessa, Darkness of the Heart" and "Phantasma." According to ANN, FUNimation has not made any announcements regarding their acquirement of these bonus episodes.
Personally, I think this is a good way to go for the industry. These "video only" episodes. Assuming the DVDs aren't ripped (which is probably assuming a lot, honestly), it's a decent way to counter against torrent viewers. Boost the DVD sales for people who have either already seen it on TV, or who have downloaded all the fansubs. I'm all for that, if it keeps the industry alive.
Spice and Wolf had an extra DVD only episode as well. I'm not sure what other shows have done the same, though I'm certain there are others.
By the way, while the anime is being distributed by FUNimation, the manga, which is also quite excellent, is being (horrendously slowly) released by ADV. They're up to volume 6 now, out of 8, I believe. Should only take them another 3 years to get those last ones out.