You really must read Petshop of Horrors -- it's excellent.
Shin Pet Shop of Horrors fits too, between the protagonist of the main story and his new supporting lead, but it hasn't been completely scanlated or published in English.
diece -- Sort of. They used to be best friends, but the circumstances of the plot force them into a rivalry/enmity.
Shuuten Unknown fits perfectly.
Number,
Adekan,
Kamui -- Between the MC and the primary antagonist.
Spiral - Suiri no Kizuna,
Loveless -- Between the protagonist and his brother. (They never really behave like siblings, so these titles still fit your request... I hope)
Vampire Library -- It's early days still, so I'm not 100% on this one.
Edit : Found some more:
Aegis -- More hatred on one side than the other, so a bit of an iffy rec.
Legal Drug +
Drug & Drop -- Between the 2 male leads.
Tsubasa Reservoir Chronicles -- Fay and Kurogane, totally.
xxxHoLic -- Kimihiro and Shizuka. Again shows a tendency towards one-sidedness.
Yami no MatsueiMacaroni -- Another perfect fit.
Tokyo Babylon has the beginnings of a literal love/hate between the MC (always forget his name because I can't stand the guy) and Seishirou, but it's better emphasized in
X/1999, which unfortunately seems to be on perpetual hiatus. And while we're on the subject: X/1999 itself has this between Kamui (the MC) and his BFF/enemy-of-sorts Fuuma.
And dear god, I can't believe I almost forgot to mention
Eroica yori Ai wo Komete! Dorian and the Major's relationship is pretty much the epitome of love/hate between two guys. Scanlations have ground to a halt at 17 vol.s (out of 39, IIRC), but what little has been done is still absolutely worth the read; it's episodic, anyway,
Junjou Karen na Oretachi da! -- I read this ages ago, so apologies if it isn't exactly right. IIRC, they eventually become pretty good team-mates, though never actually friends.
Wild Life -- The protagonist and a fairly major side character.
Burning Hell - Kami no Kuni -- The fact that this was cancelled still makes me sad. I do recommend reading the 4 chapters that were put out, though. Fits your request very well.
Gakkou no Sensei -- A fox-boy and a rabbit-boy, believe it or not
They don't have very important roles so far in the plot, though. Shame, 'cos imo they're pretty much the only really interesting characters in that story.
Cantarella,
Seimaden -- If my memory isn't playing tricks on me.
Midnight SunGankutsuou -- An anime, but a pretty good fit.
Kootetsu no Hana -- Some of the comments compare the relationship between the MC's to Naruto and Sasuke's friendship/enmity, actually.
Soul to Seoul,
Nabari no Ou,
Horror Collector -- Long-ago reads, so no guarantees that these fit.
Last edited by calstine at 8:54 am, Mar 3 2015