I usually take breaks from time to time when playing Nutaku stuff, and I always notice some games vanish from list.
A list of RIP games would be a great idea to this forums, I will try to add those I remember:

(straight from their blog)
Kanpani Girls
Shooting Girls
Quiz of Valkyrie
Angelic Saga
Hitsuji Chronicle
Omega Zodiac
DDTank 3
Hellfire Girls
Girls Kingdom
X-overd

(others)
Idol Wars Z
Phantasma Magic Deluxe (Wand & Wood)
Narborian by Night
Sengoku Providence
Osawari Island
Mononofu ~ White Lily Battle Princesses ~


Help me by adding titles I didn't list here