Black Mage and Fighter from 8-Bit Theater. So...Fighter McWarrior and Blackmage Evilwizardington have been travelling together for probably years. No matter what made BM do that, it definitely qualifies them for the trope and if Fighter knew what heterosexual meant he'd probably describe their friendship like that. At least, Fighter would. Black Mage would stab Fighter a few dozen hundred times to illustrate his point as he said no. He would then probably Hadoken or evilstab the questioner. If Fighter's memory is to be trusted, they have been "best buds 4-eva" since when they were both kicked out of their respective schools, and in the epilogue continue to adventure together 3 years later.
Axel and Zexion in Ansem Retort. They're so close that Zexion was able to hit on Axel's wife — during their wedding — and not suffer a horrific death.
Arthur and Lancelot in Arthur, King of Time and Space. Which is... kind of awkward, in the circumstances, though it depends on the timeline. The "fairy tale" timeline strains their relationship the greatest, and they were never friends in the M*A*S*H parody line. The present-day and sci-fi timelines (especially down the road a few years) treat it as just a fact of their relationship - they both love Guinevere and each other too much to let it get in the way, and it's usually only a problem if someone else makes it a problem for them (like, say, political realities of their relationship or someone trying to reveal the queen is "unfaithful"). (The final storyline reveals Arthur loves Lancelot exactly the way he loves Guenevere).
Rittz and Skip in Boxer Hockey have been friends since childhood and still live together.
Bloody Urban has two sets, the first being Murray and Shaz, and the second Libby and Angelica (who are living together to boot).
Rob and Jamie in Distillum are brothers in everything but blood.
Bumper and Stunt of Dominic Deegan - this has been noted by other characters in the series, often to tease Stunt, a staunch homophobe.
Elliot and Tedd in El Goonish Shive, driven home by the fact that, in an alternate universe where Elliot was born a girl, they're dating. Later revealed by Word of God to be true in nearly every alternate continuity where they are both alive and sexually compatible. Which is probably why Lord Tedd is such a grumpy gus - no Elliot and no relief (his "Grace" is an extremely large (and male) squirrel hybrid by the name of General Shade Tail).
Emergency Exit has quite a few relationships like this, the most obvious being the main characters and roommates Bob and Eddie, as well as Karl and Jason even though Jason technically expressed romantic interest in Karl, but since Karl's straight, they are only very close friends.
Gamma and Zimmy's relationship is simultaneously sweet and toxic: On the one hand, Zimmy would gladly die if Gamma asked her to; on the other hand, she poisons other people's friendships with Gamma to ensure she never leaves. It really doesn't help that Gamma is about the only thing that keeps Zimmy from freaking out and bad shit happening. Word of God is that they are together, romantically but not sexually, but in the comic itself, they're "only" this.
Annie and Kat, to the point that their relationship is frequently used as a symbolic representation of the harmony between the Court and the Forest. Not heterosexual, however, as Kat and Paz start dating in Chapter 42 and Annie comes off more asexual than anything else.
Donald Donlan and James Eglamore. Surma noted in one flashback that when Jim was away for training, Donnie seemed to miss Jim more than she did. Surma was Jim's girlfriend at the time.
Surma and Anja (Annie and Kat's mothers). It was due to this reason that Surma insisted on her and Anthony leaving the court during her pregnancy; she couldn't bear the thought of Anja watching her slowly waste away after Annie's birth. It broke both their hearts.
Casimiro and Finas of Hanna Is Not a Boy's Name have been together for centuries even though they are polar opposites in personality. Cas describes their relationship as "too unique to put a label on", but says yes, Finas is his best friend.
John and Dave, despite never meeting in person. Their given names being the shortened forms of Jonathan and David is likely not a coincidence. The moirallegiance quadrant of the trolls' romance system combines this trope with elements of Morality Pet, though it's not restricted by gender at all and the most prominent examples are boy-girl.
Mandatory Roller Coaster infrequently features two unnamed men who are always drinking at a bar together.
MegaTokyo: Piro and Largo, and Kimiko and Erika. All are canonically straight, but each pair lives together, and have done so at least since college.
Ménage à 3 has Maura and Tess, two former school friends who competed together as synchronized swimmers, switched to become a wrestling tag team, and share an apartment. Their friendship is strong enough to survive a little mutual snarking and occasional competition for the same guy, and even when they fight, seemingly seriously, they can't stay angry for long.
Roy and Durkon of The Order of the Stick are probably the closest members (in terms of friendship at least) of the Order. Their backstory comic reveals that the two became friends over two years before the Order was founded after Roy refused to kill a group of Evil-aligned orcs for XP because they technically weren't doing anything wrong. This attitude impressed Durkon, and they were friends ever since. When Durkon is temporarily killed, the news of his death hits Roy the hardest out of everyone, and he almost crosses the Despair Event Horizon before Belkar manages to snap him out of it.
Sakana: Jiro and Taisei have been best friends since middle school, and they are practically inseparable, go shopping together and share an apartment, and after Jiro finally goes on a date with cashier girl, Taisei can't stop worrying about him getting hurt, and so he stalks their date. The artist also stated that Shigeru and Taro are "bros for life", and it shows.
The main character 9 and his best friend Chuckles, in Serious Emotional Disturbances. Lampshaded at one point during a reunion scene with a Celine Dion song being played as the two run towards each other. So much so that the town of Bumfuck (where they live), including 9's evil Gramma, assumes the two are gay for each other.
Torg and Riff from Sluggy Freelance. Though even after being best friends for decades, they're still not that comfortable with hugs. Zoe and Gwynn too, for that matter.
Terinu and Matt. They spent half their young lives together as the abused slaves as a pirate warlord, with Matt stealing food to keep Teri healthy and at one point he cuddled in bed with him after Terinu's powers were traumatically activated. Wordof God has stated "Both of them would rather be dead than see the other hurt."
Yu Hansung: Since Ro has left, I guess I should fire you, too. Since you two are a set menu, like a hamburger and a cola. It would be inhumane to separate the two of you. I hope you continue your beautiful love forever and ever.
Levana and Laura from Vampire Girl. For the longest time, Laura was the only real friend Levana had when she was a vampire, and even long after she became a mortal, Laura continues to be particularly supportive of Levana, even getting rather miffed when Levana disappears and nobody seems to be too overly concerned for her wellbeing.
Ben and Alex from Weak Hero. The two have been inseparable friends since childhood, and hurting or insulting one of them is the one surefire way to piss the other off. Gerard teases them about it in their first meeting, saying the two look good together.
◊ from Lackadaisy. At least, until Mordecai found a better job and shot Viktor in his good knee on the way out. Having a murderer for a partner carries a certain degree of risk.
