Wow, I definitely love this thread. Partly for the fantastically long list of great recommendations, but also because it's just great to know there are so many other lovers of gay subtext out there. I like realized gay relationships too, but the subtext ones allow these relationships to exist in so many places where they otherwise couldn't.
Anyways, I don't have a whole lot to add since most of the ones I know of have already been mentioned, although I would like to reiterate the recommendation for
Cotton, since I love that manga and it only got one mention early in the thread. In the truest sense it could never be considered subtext, the yuri relationship is pretty much the focus of the story, but it's also not fully realized and never consummated. I guess it just depends on how subtle you want the relationship to be.
Also, it's kind of off the beaten path, but
not simple is another great manga with a beautiful unrealized gay relationship. It's been a while since I read it though (and I rushed through it too much), but if I remember correctly it's pretty one-sided in that one of the men is straight and expressed interest in women, but I still found it wonderful nonetheless.
Strawberry Shake Sweet is a cute little story of (mostly) unrealized GL. I found it a bit frustrating, because there was too much longing with absolutely no acting on it, but I've heard from others that really liked it, so it's worth a try.
Azumanga Daioh kind of strays from your requirements in that the more blatant subtext of the series is between a minor-character and a main-character, and given the gag-driven nature of 4-koma manga it never really
develops, but I'd recommend it nonetheless. The whole thing is rife with potential subtext (if you're wearing your Yuri Goggles) in that pretty much all the named characters are female. It's worth a read anyways if you want a fun little 4-koma manga, but the subtext is an added plus.
If the
K-On! anime was following the manga closely then there should be some yuri subtext in that 4-koma as well, but I haven't read past the first volume yet, so I can't say for sure. Although, even if it doesn't have the more blatant subtext from Mugi that the anime had the close relationship between Mio and Ritsu is pretty much canon-level yuri subtext anyways.
Anyways, those are the only ones I can think of for now that haven't been mentioned. Thanks to everyone else for all the recs -- my reading list just got a lot longer.