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For the last two years or so, I've gotten repeated requests to unequivocally name my top VNs made up until the present, ignoring objectivity, my vndb votes, etc.  I've more or less just ignored most of those requests, because it is a pain in the ass to name a 'favorite' VN in the first place.  I've made lists of VNs I loved from various genres, and I've also made lists of VNs for a specific purpose.  However, I've avoided making a list like this one up until now, mostly because my 'favorites' switch out so often. 
Let's get this straight for those who are going to criticize my choices... these are the VNs I like the most, not the fifty best VNs of all time.  I make no pretense to preeminence of opinion in this case, because I'm also discarding all attempts at objectivity.  What a person likes is ultimately a matter of personal tastes, not a matter of logic.
Why did I make it fifty?  Because my number of VNs played, setting aside replays and nukige, is over six hundred already (with replays and nukige, it is closer to eight hundred...)... I'd be surprised if I didn't have this many VNs I considered wonderful. 
Keep in mind that these aren't in a particular order.
 
1.   Evolimit
2.   Dies Irae (the one by Light)
3.   Ikusa Megami Zero
4.   Nanairo Reincarnation
5.   Semiramis no Tenbin
6.   Bradyon Veda
7.   Vermilion Bind of Blood
8.   Hapymaher
9.   Tiny Dungeon (as a series)
10.  Bullet Butlers
11.  Chrono Belt
12.  Ayakashibito
13.  Otome ga Boku ni Koishiteiru 2
14.  Chusingura
15.  Draculius
16.  Otome ga Tsumugu, Koi no Canvas
17.  Silverio Vendetta
18.  Konata yori Kanata Made
19.  Grisaia series
20.  Akatsuki no Goei series
21.  Reminiscence series
22.  Haruka ni Aogi, Uruwashi no
23.  Harumade, Kururu
24.  Soukou Akki Muramasa
25.  Tokyo Babel
26.  Tasogare no Sinsemilla
27.  Komorebi no Nostalgica
28.  Yurikago yori Tenshi Made
29.  Izuna Zanshinken
30.  Moshimo Ashita ga Harenaraba
31.  Kamikaze Explorers
32.  Devils Devel Concept
33.  Suzunone Seven
34.  Baldr Skydive series
35.  Baldr Sky Zero series
36.  Toppara Zashikiwarashi no Hanashi
37.  Tsuisou no Augment (series)
38.  Kikan Bakumatsu Ibun Last Cavalier
39.  Shin Koihime Musou (series not including the original Koihime Musou)
40.  Soshite Hatsukoi wa Imouto ni Naru
41.  Tenshi no Hane o Fumanaide
42.  Irotoridori no Sekai
43.  Noble Works
44.  Koisuru Otome to Shugo no Tate (series)
45.  Kitto, Sumiwataru Asairo yori mo
46.  Jingai Makyou
47.  Sakura, Sakimashita
48.  Abyss Homicide Club
49.  Re:Birth Colony Lost Azurite
50.  Owaru Sekai to Birthday