With Marvel announcing that they were making an online archive of their comics available to subscribers, I though it'd be worth noting the company's significant moments in its history with gay characters. Since Marvel doesn't have a complete list of all the comics available to subscribers, I can't tell if any of these comics can be read through the new service. However, if the service succeeds, hopefully it'll get more content to offer. (I'd be tempted to subscribe in that case -- there are plenty of "So bad it's good" stories from the grim 'n gritty era that I might enjoy reading but wouldn't care to own.) There's a little bit of good, a little bit of bad and a lot of "Well, it was progress at the time." In order to keep the best moments above the cut, let's start with the most recent events:

Hulking and Wiccan's (semi-)botched coming out
From: Young Avengers #7 (2005)

A lot of the buzz on the early issues of Young Avengers focused on the relationship between Hulkling and Asgardian. Their banter sounded a lot like a superhero couple, but since the early issues of Young Avengers didn't show the team's downtime, there was plenty of room for debate (including speculation that Hulkling would turn out to be an young woman drawn to look sexually ambiguous) if they really were a gay couple. Part of the confusion came because superhero comic readers still aren't used to seeing same-sex couples written the same as an opposite-sex couple, so when a couple of gay characters were introduced without fanfare it was still surprising. Soon after the relationship between the two young men became clear, the team decided they had to let their parents know about their superhero activities. However, Billy and Ted's attempt at coming out was mistaken for a more typical kind of coming out. The title would later go on to be one of the few Marvel titles to win a GLAAD media award, which frequently goes to independent or DC titles.

Ultimate Colossus is finally outed
From: Ultimate X-Men #65 (2005)

When Marvel introduced the Ultimate Universe in 2001, it introduced familiar characters and stories with new perspectives and twists. For years Ultimate X-Men readers got hints that the Ultimate version of Colossus was gay -- most involved Colossus playing to stereotypes or teammates making snarky comments about Alison Blaire's chances with him (she had an obvious crush). When we finally got confirmation of Colossus' sexual orientation (in the form of him accepting a date with Northstar) it was a pretty welcoming moment, especially since the mainstream version of Colossus was a character that straight, male readers of X-Men titles identified. A safer choice could have been made for a mutant to be re-imagined as gay, but Ultimate X-Men creators happily picked Colossus.

Things get a little more bitchy after the break:

The Rawhide Kid is re-imagined as gay
From: The Rawhide Kid (2003)

When Marvel introduced its short-lived Max line of comics aimed for Mature Readers, that included a number of titles that mixed familiar concepts with "mature" amounts of violence and sexuality (which, sadly, did not include a promising Buffy-inspired revamp of romance comic Night Nurse). In 2003, Marvel drew media controversy over a mini-series that saw Western comic icon The Rawhide Kid as gay. Unfortunately, many readers were disappointed to find that the comic was fueled by stereotypes and innuendo-based humor. Worse, there was little meriting the "Explicit Content" warning aside from the acknowledgment that the character was gay, suggesting a double-standard.
The title got plenty of media coverage thanks to controversy from anti-gay media activists who think of comics as a medium belonging strictly for children. One popular (and politically conservative) writer, Chuck Dixon, even accused Marvel of tricking The Rawhide Kid's artist into working on the gay-themed comic. Three years later, the series ignited more controversy when Marvel Editor-In-Chief Joe Quesada mentioned in an interview that, due to the Rawhide Kid furor, any title starring a gay character would have to have a "Mature Readers" warning -- a comment that left some worried (since Marvel wasn't publishing Mature Readers titles anymore) that gay characters were being specifically excluded at the publisher.

Northstar comes out
From: Alpha Flight #106 (1992)

The coming out of Northstar was a mixed bag. It was an important moment in terms of gay visibility, but it had so many downsides. Most importantly, the story fully falls into so-bad-it's-good territory. The comic stars with Northstar's team, Alpha Flight, finding a baby infected with HIV. When he decides to care for it, the positive media coverage angers a retired Canadian superhero, Major Mapleleaf, into attacking Alpha Flight. The Major's fury, it turns out, is fueled by memories of his son's death from AIDS complications, a death ignored by the media because it happened to a gay man (making him hate HIV-positive babies who get better treatment in the media). Northstar defuses Major Mapleleaf's anger by announcing that he, too, is gay. No, that issue does not make any more sense if you read the actual comic.
Beyond that, however, the story brought about other problems. The story happened to coincide with the writer leaving the series, a coincidence that fueled speculation that he was fired for the story. The way Northstar was handled afterwards was also pretty bad, with stories that included an illness (that was meant to be revealed as AIDS), an unrequited crush on a straight man and a controversy-courting storyline where he dies and comes back.

Larry Bodine's suicide
From: New Mutants #45 (1986)

While not specifically gay-themed, the powerful "We Were Only Foolin" was a major moment for gay readers. It told the story of Larry Bodine, a student picked on at his high school for being the new guy. He is taunted by bullies who call him a mutant as a generic insult, but it turns out that Larry actually is a mutant. Thinking his secret is known and unable to figure out how to deal with being a mutant, Larry kills himself. The story ends with one of the most moving scenes in X-Men history when Kitty Pryde eulogizes Larry:

Who was he, then, that we gather to mourn him? Who am I? A four-eyed, flat-chested, brat, chick, brain, hebe, stuck-up Xavier's snob freak! Don't like the words? I could use nicer. I've heard worse. Who here hasn't? So often, so casually, that maybe we've forgotten the power they have to hurt. Nigger, spic, wop, slope, faggot, mutie--the list is so long. And so cruel. They're labels. Put downs. And they hurt.

Aurora meets Raymonde
From: Alpha Flight #7-8 (1984)

For years, an early scene from Alpha Flight's history was all we had in showing that Northstar was meant to be gay. In the two-part story he introduces his sister to a "special friend" who Aurora isn't so quick to accept and is, instead, quick to condemn for his influence on her brother. When Raymonde is later killed by a supervillain, Northstar's reaction is very strong, furthering suspicion that there was more to the relationship than being just friends. In hindsight, a lot of the hints towards Northstar's sexual orientation plays to gay stereotypes but at the time it was a major step towards gay inclusion.

Bruce Banner is nearly assaulted in a YMCA shower
From: Hulk Magazine #23 (1980)

This story by former Editor-in-Chief Jim Shooter is seen as a notable low point for Marvel's treatment of gay characters. While positive depictions of openly gay characters weren't allowed at the time, that didn't seem to exclude a story where a couple of effeminate men seem intent on sexually assaulting Bruce Banner in a YMCA shower.