As a big fan of the school genre, I'm very interesed in this thread.
For male characters:
-The gakuran uniform which its much more common in middle-school (or junior high school) and formerly senior high school uniform by default, I prefer it for school series in middle school rather than (senior) high school series due another type of uniform make high school male characters different from the middle school ones. For high school, I prefer much more when male characters wear blazers/jackets, a white shit and a tie, they made them more unique.
Since I don't really like the gakuran uniform very much, I have very few series to choose with this type of uniform for high school series but I'll go with Hyouka, Bakemonogatari and Love is War series since I think they are one of the few high school series where the gakuran look quite good on them and it doesn't felt like aged awful like YYH gakuran uniform and unlike other series where the male uniform look awful on them meanwhile the female uniform was made better on purpose like Toradora!, Haikyuu!! and Charlotte. I'll not mention any for middle school series since almost all gakuran uniform tend to be the same.
For male characters with blazers/jackets, I have so many to choose. My favourite uniform colour for them tend to be either red/black/blue blazers, red, blue or black tie and generally black pants. Depends of the school uniform, a tie isn't even necessary like Hachiman from Oregairu or Touma from the Index series look quite good without it. I tend to like darker colours here or a very least a combination of dark and light colours, so my favourite male uniforms for in this case are from the series (in order, some of them are not school series):
1) ONK: probably one of the best since I don't really remember any series where a purple blaze look too well especially when Aqua wearing those clothes. Too bad it isn't a school series since I wanted to see more of the uniform. Also, I like the author decide to use a very different uniform from Love is War series making both series unique in that aspect.
2) Classroom of the Elite: the best school series with the best male uniform, hands down. I'm a massive COTE fan so I'm not surprised I love this uniform. Green + red = peak.
3) Kakegurui: perfect combination of red brazers and black pants. It's better since the uniform for both sexes is obviously based in the theme of the series itself making the uniform a combination of croupier uniforms, gambling addiction and casino.
4) Haruhi Suzumiya series: probably the best school series where dark brazers and brown pants look quite good. It's the most simplistic looking male uniform which I rate higher than others due they look so good.
Others good examples Love, Chunibyo & Other Delusions, Little Busters (never watched the series but love the uniform), Rakudai kishi no cavalry, Boarding School Juliet, Liar Liar, Masamune revenge, Horimiya, Free!, Kimi ni Todoke, Food Wars, Kage no Jitsuryokusha ni Naritakute (not a school series), Bunny Girl Senpai, Maid-sama!. For this type of uniform, its very hard for me to dislike it but some series which I really dislike the male uniform in: To Love Ru, Evangelion (not a school series), Clannad s1, my dress up darling (pants are ugly), MHA (iconic shounen but pants colours don't look well on them), Angel Beats! (I love the series but never liked the uniforms, bad colours combination), Mahouka Koukou no Rettousei, Fruits Basket (seriously, the worst male uniform I've seen in a school series, awful colours and design as least in the male side).
Special mention to JJK which I like the series but I don't like the uniform they wear, I know it isn't a typical school series but the uniform design isn't good. Colours are slighty better unlike MHA weird pants lol.
For female characters: i care very little about their uniforms besides I don't like female uniforms in general so much and most people in this thread were more focused in that aspect than me so I don't have much to add. Mahouka Koukou no Rettousei and Madoka Magica have the best female uniforms.