BioWare has acquired a certain degree of fame (or infamy) in the video game industry for their LBGT Fanbase, Gay Option romance sidequests, and Bi the Way party members / NPCs/ PlayerCharacters, as well as their spirited defense of all of the above. So if you see Ho Yay in a BioWare game, chances are it wasn't accidental.
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In the first game, Alistair is pretty good for this if you're playing a male. Taking a certain aggressive dialogue option results in him saying (most likely sarcastically, but still) that you're cute when you're angry. Note that he doesn't say this if you're a female PC. As well, if you romance Morrigan, who Alistair hates, he gets into an argument with her about you. Morrigan teases him about being jealous of her, referring to you as Alistair's "favorite Grey Warden". The best part? When she says this, he blushes!
All love interests (except Sebastian) are bi in Dragon Age II, but it doesn't necessarily stop with them. Aveline, post Matchmaker Quest, can ask Hawke if there might have been something between them regardless of gender.
Varric: If you have something to say, just spit it out.
Anders: Are you sure you want to encourage me? I might be about to confess my undying love.
Varric: (unfazed) I get that a lot. So what's on your mind?
While it wasn't until Mass Effect 3 that the first careful steps where made to have a gay man appearing and actually spelling it out, the side Quest with the Viscounts son in Dragon Age 2 seems to be set up in a way that you can see a very strong gay subtext if you want to, but it could also be completely nonexistent if that's your interpretation. But given that he repeatedly runs away with his muscular and exotic friend and the two of them hide out in the wilderness alone rather than staying with other Qunari in the region casts at least some doubt on his claim that he wants to learn about Qunari culture and that his fathers people should try to find ways to peacefully coexist with them. He also takes it as a personal loss when the Qunari is killed and not as a setback to his diplomatic efforts. If it had been the Viscounts daughter, there wouldn't have been any doubt what's really going on. This was eventually confirmed by Word of Gay.
Predated by Herren and Wade from Origins and Awakening, where the subtext was much more overt, though not explicitly stated in the game. After much speculation, this was also confirmed by Word of Gay.
Not surprised. Stanley Woo (Juhani's writer) explicitly stated that he intended Juhani to be not only gay, but the Gay Option. Lucasarts was not happy, leading to him dialing it down, but sneaking it in, anyway.
Let's not forget about perpetually grumpy Jedi Belaya, who can be seen power walking around the main plaza inside the Jedi enclave. She seems to have more than a friendly relationship with Juhani, and if you kill off Juhani in the grove, she goes Psycho Lesbian on you, says some very texty things, and the next time you see her, she's joined the Sith Academy on Korriban and is out for your blood. But surely that can be attributed to wanting revenge for a platonic friend, right?
Play female and talk to Juhani about Quatra in the grove. She will remark "In my own way, I truly loved her." It could be "merely" read as the whole Master/Padawan dynamic (the only love a Jedi is really allows to have), but Courtnay Taylor was apparently handed the memo about Juhani being gay. Knowing that this line is skipped over if the protagonist isn't female makes it read as a Trial Balloon Statement.
Canderous declaring "I'm your man until the end" if you play a male Revan. This really isn't helped when Kreia in the sequel starts delivering a Breaking Speech to him with lines like "Do you wonder where he wanders now, Mandalore? Why he gave you your orders, then abandoned you at the edge of the galaxy?" Furthermore, Expanded Universe material says that not only do the Mandos not particularly care about sexual orientation, but that (spoiler for Revan) Canderous shot his own wife to prevent her from killing Revan.
Mass Effect 1. Sure, there's the canonical stuff (if you wish to pursue it) between female Shepard and Liara, but subtext-wise there's male Shepard/Kaidan. There are some lines to support it as well ("When it's just you and me, Alenko, consider it off the record..."), especially if you choose to save Kaidan over Ashley.
Liara T'Soni quickly develops a crush on Shepard regardless of gender, and her pairing with a female Shepard is one of the more popular pairings of the fandom. Their respective voice actresses, Ali Hillis and Jennifer Hale, took it one step further by having massive Les Yay during interviews.
Mass Effect 2 also features massive amounts of Les Yay between female Shepard and Tali after earning Tali's loyalty - Tali confesses that the most intimate thing a quarian can do is link their environments, their most important gesture of trust and acceptance. She hasn't trusted anyone enough for that, though, except... well, no quarians. Shepard can either teasingly ask if she's blushing and get first a flustered reaction, then an exaggeratedly petulant response, or Shepard can say she feels the same way but Tali doesn't have to prove anything. In that case, Tali says, "Nevertheless, I'd be honored to link suits with you, Shepard. You know, if you were a quarian and we weren't already on a suicide mission." Either way, she ends the conversation with a flustered excuse.
It's clearer once you've played through as a male and gotten to that point, and she tells male Shepard that the tradition also signifies a willingness for... intimacy, then says it's not always like that.
Further evidence is found in The Lair of the Shadow Broker DLC: after getting access to Shadow Broker's secret files, Tali's folder will reveal that she's been repeatedly activating and turning off her suit's "neural stimulators", and gathering information about human mating practices, after you complete her loyalty mission - completely regardless of Shepard's gender!
Discussed when you speak with MordinSolus constantly in Mass Effect 2 and if you're not romancing anyone. While a largely asexual individual, Mordin remarks that if he ever wanted to try a human, he would try Shepard. And yes, he says this to Shepard no matter the gender.
Seeing him changed my life, woke up something in me I don't fully understand yet. I don't know what I'm going to do, but salarian lives are too short to waste as custodians, especially when there's so much else out there. I'm going to find something that lets me capture what I saw in him, that beauty, that aesthetic perfection.
I'm also going to buy some nice clothes.
So if you could tell him that... or just whatever parts of that you think appropriate... I'd appreciate it.
Mind you, that e-mail was a Shout-Out to a particular fan on the old BioWare official forums, who was well-known there for her love for Thane before the game was even out (and the e-mail is in reference to her particular style of posting). But, as most of the salarians seen in-game are male, technically it still counts as ho yay.
Upon re-meeting Garrus his dialogue sounds weirdly intense, and he all but admits to being utterly lost without you. If you choose to wander about in between enemy waves, he'll say "I need you, Shepard" every ten seconds.
Mass Effect 3 makes Kaidan an official romance for male Shepards. The fans saw so much Ho Yay between them that they campaigned in the Bioware forums to make it happen, and Bioware went Ascended Fanon and created the option. This does not apply to female Shepards and Ashley, since there wasn't such a demand for them.
Lieutenant Steven Cortez, the Kodiak pilot and the other Gay Option, seems to have a bit of a flirtatious relationship with the new recruit James Vega, who is stationed on the floor as him. When you talk to either one of them, often times they will call out to the other during dialogue, often teasing each other somewhat flirtatiously.
Shepard: Do you maintain this armory?
Cortez: I share that duty with our illustrious Mr. Vega. (yelling to him across the room) Though I believe the only weapon he cares to maintain is himself!
Vega: (doing pull-ups) You know you like the show, Esteban!
Also in the last mission, if Cortez dies because you didn't complete the friendship/romance path, then James ends up completely flipping out.
The dialogues between Aria T'Loak and the turian biotic Nyreen in the Omega DLC suggest that their past relationship went past mere attraction and annoyance they claim it to have been. Later on, Nyreen turns her back to the enemies to protect Aria, while Aria flies into an outright Unstoppable Rage when Nyreen is killed. And if you go for the Renegade solution, Aria will kiss you; people have timed it, and female Shepard gets a significantly longer one.
At the party after the main events of the "Citadel" DLC, Miranda and Jack (who have been at each other's throats since ME2) find themselves seated across each other at the bar, trading insults (and occasional grudging compliments). Assuming Shepard romanced neither of them, he/she can actually call them out on this Belligerent Sexual Tension and suggest they just make up and make out. Both of them seem confused by, though not immediately opposed to the idea.
Garrus/Male Shepard has some fairly strong hints as well. This gem during the Citadel hangout says it all:
Garrus: You're not going to propose marriage now, are you?
In Citadel, Kasumi can be found at one point searching through Shepard's underwear drawer, which occurs with both genders.
Star Wars the Old Republic
An optional romance sidequest can be accessed on Makeb with wither Dr. Avesta (Republic) or a minor Sith Lord (Imperial). The dialogue and romance option are fully playable, regardless of the player character's gender.
Two of the informants on the Bounty Broker quests are very open to flirting, gender optional.
Mako gets plenty of it with a female Bounty Hunter. A sign she will become a Gay Option in an update, post-release?
Watcher Two also gets some of this with the female Agent.
For male Agents, this is subverted with Hunter, who turns out to be a woman.
During the initial questline for Sith Inquistors, you are given tasks by one Overseer Harkun. He compares you, very unfavorably, to another acolyte named Ffon, a Sith Pureblood. While this could be an example of Fantastic Racism, the fact that he does it it nearly every cutscene makes a few players wonder...
A blink-and-you-miss-it reference during the Republic Oricon questline. One of the soldiers reports having nightmares about shooting his husband.