Bioshock 1&2 come to mind. Remove the entirety of Infinite save Burial At Sea (the only good thing to ever come out of the game) and we're golden. The duology - because yes, that game does not in fact exist to me - stands as a milestone in my love of gaming, adore just about everything from the atmosphere, to the gameplay, to the details the devs put into Rapture feeling alive despite being long gone and decayed.
Perfect games? Nope, such a thing doesn't exist, they have their quirks and shortcomings. But they are high up for me and I love replaying them.
Edit : Should also mention SH2 and RE2. Enough has been said about these games, but my only qualm is being unable to play either in their original format on modern hardware in the EU.
For manga, Slam Dunk. The story should have went a less bittersweet route with Shohoku's last match actually being shown instead of Inoue giving us a half-assed explanation as to why things went like that. It is a very solid series to breeze through.
Malcolm In The Middle is my favorite show, but I really do think the grown-up seasons were less entertaining than the earlier ones. IMO it should have ended a bit sooner, before more kids came into play. That was when I began struggling with its' writing.
Blade Runner for movies. The fact it's been 40 years and a new Ultimate Workprint Ultra-Deluxe Director's Cut still keeps resurfacing is getting tiresome. Just give us a real definitive format, that movie's amazing without five additional seconds of Harrison Ford eating a bowl of noodles or staring into L.A.'s polluted sky.