Angel's Egg (1985) -- OVA

Maison Ikkoku (1986) -- TV-Series/Movie

Patlabor (Mobile Police Patlabor) (1988) -- OVA

Patlabor the Movie (Mobile Police Patlabor) (1988) -- Movie
Ranma 1/2 Series (1989) -- TV-Series/Movie/OVA

DNA^2 (1994) -- TV-Series

Kishin Doji Zenki (1995) -- TV-Series

Rurouni Kenshin (1996) -- TV-Series
Violinist of Hameln (1996) -- TV-Series
You're Under Arrest (1996) -- TV-Series

Eat Man (1997) -- TV-Series
Haunted Junction (1997) -- TV-Series

AWOL (Absent With Out Leave) (1998) -- TV-Series
Dainagiga (1998) -- OVA
Eat Man 98 (1998) -- TV-Series
Momoiro Sisters (1998) -- TV-Series
Urayasu Tekkin Kazoku (Weird Family) (1998) -- TV-Series

Edens Bowy (1999) -- TV-Series
Rurouni Kenshin Tsuiokuhen (1999) -- OVA
Soul Hunter(Senkaiden Hoshinengi) (1999) -- TV-Series
You're Under Arrest the Movie(1996) -- Movie

Gravitation (2000) -- TV-Series
Mon Colle Nights (Monster Collector Nights) (2000) -- TV-Series

Fruits Basket (2001) -- TV-Series
Kokoro Library (2001) -- TV-Series
Rave (2001) -- TV-Series
R.O.D ~Read Or Die~ (2001) -- OVA
Rurouni Kenshin Seishohen (2001) -- OVA
Sadamitsu (2001) -- TV-Series
Star Ocean EX (2001) -- OVA
You're Under Arrest 2nd Series (2001) -- TV-Series

Bomberman Jecters (2002) -- TV-Series
Get Backers (2002) -- TV-Series
King of Bandit Jing (2002) -- TV-Series
Samurai Deeper Kyo (2002) -- TV-Series
Search for the Full Moon (2002) --TV-Series

Mouse (2003) -- TV-Series
Mythical Detective Loki Ragnarok (2003) -- TV-Series
Yami to Boushi to Hon no Tabibito(The travel of Darkness and Hat and Book) (2003) -- TV-Series

Get Ride! AMDRIVER (2004) -- TV-Series
King from Now On!(Kyoukara Maou) (2004) -- TV-Series
Kitahe ~Diamond Dust Drops~ (To the North ~Diamond Dust Drops~) (2004) -- TV-Series
Marimite (2004) -- TV-Series
Marimite 2nd Season ~Spring~ (2004) -- TV-Series
Tactics (2004) -- TV-Series
Yumeria (2004) -- TV-Series
Zipangu (2004) -- TV-Series

Ameanaideyot!! (2005) -- TV-Series
Gingadensetsu WEED (2005) -- TV-Series
Law of Ueki(Ueki no Housoku) (2005) -- TV-Series

Binchotan (2006) -- TV-Series
Fate/Stay Night (2006) -- TV-Series
Higurashi Naku Koro ni (2006) -- TV-Series
Marimite 3rd Season (2006) -- OVA
Princess Princess (2006) -- TV-Series
Shounen Onmyouji (2006) -- TV-Series
Simoun (2006) -- TV-Series

CODE-E (2007) -- TV-Series
Higurashi Naku Koro ni ~Kai~ (2007) -- TV-Series
Shining Tears x Wind (2007) -- TV-Series
Shion no Oh(The Flowers of Hard Blood) (2007) -- TV-Series
Suteki Tantei Labyrinth(Nice Detective Labyrinth) (2007) -- TV-Series
Toukagettan (2007) -- TV-Series
You're Under Arrest Full Throttle (2007) -- TV-Series

Hong's Personal Comment : It takes a long time to list all the famous animes produce by Studio Deen. Since it has long history of anime production, you can expect something more than average quality. Different from these day's productions, Studio Deen does not have particularly strong point, but it does not have particularly weak point also. This seems to be both good thing(we can expect certain level of quality all the time) and bad thing(it is hard to give some impact).
I would say that Studio Deen has both ability to depict the characteristic of original work and ability to produce its own anime original works. The former has been proven by various works such as 'You're Under Arrest', 'Marimite', 'Higurashi ~Kai~', 'Rurouni Kenshin', etc. The latter is proven most by 'Simoun'.
Even though it has long history of production, it does not stops to try new experiments. In 'Yami to Boushi to Hon no Tabibito' and 'Toukagettan' it has shown very experimental way of storytelling, which is still on the controversy among the fans.
I personally like so-called 'Yuri' animes produced by Studio Deen : 'Marimite' Series, 'Yami to Boushi to Hon no Tabibito', and 'Simoun'. Especially, in case of 'Simoun', its original production, I would assess that this is the best anime of 2006, even though its 'yuri' elements makes people hard to approach to this anime.