The magazine Newtype is Japan's best known publication for all things anime, at one point, they compiled a top 30 list for male and female characters for each decade starting from the 80s leading up to 2010s.
As this is a Japanese magazine, it's my opportunity to judge the Japanese on their taste in anime characters; I will not be judging these characters on their rank, only their inclusion on the list.
Each list will have a score out of 30 judging their taste.

Next up is the 90s
1, Ikari Shinji
Oddly yes, as bad as Shinji is, he did make an impact and it doesn't include the rebuild films as it only covers 90s.
2, Nagisa Kaworu
But I'll say no to this character.
3, Kurama
Yes, Yu Yu Hakusho was very popular.
4, Sakuragi Hanamichi
Never seen Slam Dunk but I wouldn't argue with the fans, yes.
5, Hiei
Yes, he's the emo character done right.
6, Heero Yuy
Yes, he made the Gundam Protagonist bearable.
7, Chiba Mamoru
Tentative yes, but only because he's from a Shojo and not a Shounen.
8, Himura Kenshin
Definitely a yes.
9, Edogawa Conan
Yes, I'm glad he didn't fall off in popularity against so many heavy hitters.
10, Nekki Basara
A very tentative yes.
11, Rukawa Kaede
Again, not arguing with fans, yes.
12, Porco Rosso
A fine choice for this list, yes.
13, Tamahome
Tentative yes, not his fault the anime was terrible.
14, Nike
It's a no, I've no idea who he is.
15, Li Syaoran
Little overrated but yes.
16, Urameshi Yusuke
Yep, more Yu Yu Hakusho is welcome.
17, Kasshu Domon
More iconic than you think, yes.
18, Spike Spiegel
No brainer, yes.
19, Yokoshima Tadao
Ghost Sweeper Mikami, yes.
20, Shishio Gai
GaoGaiGar, yes.
21, Duo Maxwell
Probably more popular than Heero, yes.
22, Shiro Amada
Solid choice, yes.
23, Parn
Lodess War, yes very underrated.
24, Xellos
One of my personal favourites, yes.
25, Senpuuji Maito
I've been pretty generous so far, but it's a no this time.
26, Jean Roque Raltique
Doesn't get enough interest, yes.
27, Loran Cehack
Very underrated, yes.
28, Seabook Arno
Terribly bland character, no.
29, Arslan
I'll take your word for it, yes.
30, Arima Soichiro
Kare Kano, yes.
Score: 26/30

1, Ayanami Rei
Between her and Asuka, yes, they pretty defined the 90s.
2, Tsukino Usagi
Sailor Moon, obvious yes.
3, Soryu Asuka Langley
Same as Rei, yes.
4, Kinomoto Sakura
I'm glad she made the list considering how late in the 90s she appeared. Yes.
5, Hoshino Ruri
I always believed her to be the thinking man's Rei Ayanami. Yes.
6, Nadia
Stands up really well. Yes.
7, Mizuno Ami
Most popular sailor scout. Yes.
8, Mylene Jenius
Tentative, put her in the same category as Minmay. Yes.
9, Belldandy
Definitely a yes.
10, Deedlit
She's the only character that made Lodess bearable. Yes.
11. Chacha
Fairly underrated. Yes.
12, Inokuma Yawara
I approve, nice addition.
13, Tifa Lockhart
Instantly disqualified, even if you do count Advent Children that's 00s.
14, Lina Inverse
My favourite female character in all anime.
15, Cecily Fairchild
Pathetic character. No.
16, Aino Minako
Another Sailor Scout, yes.
17, Katejina Loos
Her actions were so atrocious that the creator refused to kill her. No.
18, Allenby Beardsley
Yes, especially when she was picked over Rain.
19, Hino Rei
Probably the least liked of the original five but still say yes.
20, Mikami Reiko
Ghost Sweeper Mikami, yeah, really underrated.
21, Relena Peacecraft
I just did a article on why she was hated, course I'm going to say no.
22, Shido Hikaru
Never liked her but really iconic design, yes.
23, Kukuri
No idea who this is. No.
24, Misumaru Yurika
Between her and Ruri, they make up most of Nadesico's fan service.
25, Mōri Ran
Detective Conan, I'd say yes.
26, Tiara
Little torn with this character as her entire fanbase would be Japanese only. Benefit of the doubt.
27, Sakura Momoko
Surprisingly yes despite looking like she's from an older anime.
28, Pai
No, her design is too generic.
29, Kino Makoto
Last of the five Sailor scouts, yes.
30, Paffy Pafuricia
No idea who she is, no.
Score: 23/30

Verdict: The 90s faired alot better than I expected out performing the 80s really well but I'd say too much Gundam Heroines in the female list really drove the score down on that one. 00s is next and expect that list to be harsh.