here are some that ive really like that have > 50k members on MAL:
[from least to most popular]
Wanpaku Ouji no Orochi Taiji
Tenamonya Voyagers
Kokoro Toshokan
Gosenzo-sama Banbanzai!
Ongaku
Nurse Witch Komugi-chan Magikarte
Fuujin Monogatari
Zettai Shounen
The SoulTaker: Tamashii-gari
Giant Robo the Animation: Chikyuu ga Seishi Suru Hi
Gakuen Utopia Manabi Straight!
Futakoi Alternative
Otaku no Video
Gal to Kyouryuu
Alien 9
Yokohama Kaidashi Kikou
Tamayura [particularly after the first short season]
Oshi ga Budoukan Ittekuretara Shinu
16bit Sensation: Another Layer
Macross Plus