Let's just get this out of the way. Lokar is one big walking example of Ho Yay.
Specific example: On the episode "Surprise", he decided a 50's theme party for Space Ghost's birthday, with roles for everyone. He made Moltar his girlfriend.
On the cooking episode, Lokar once again insults Space Ghost with big words. Tansit points out he just called him beautiful in Latin. Lokar does say that his vocabulary tends to confused him as well, but that doesn't negate the fact that Brak agrees with the sentiment that Space Ghost is pretty, or his agreeing to Tansit's teasing suggestion to kiss him.
Also, on the telethon episode, Lokar offered to kiss anyone who donated. Tansit seemed interested.
When Moltar was selling stuff in Waiting for Edward, the two things Lokar asked about were a "dangerously sequeined" hot pants and a scented thong.
During the second episode Zorak shows clips from his time on Gilligan's Island. The first one, a clip with him and the Professor, he described as, "Me in courtship."
Zorak: Bill, I respect you. Professor: How about love? Zorak: ...Yeah, that too.
In "CHiPs" Space Ghost asks what a monologue is, to which Zorak says it's the part of the show where the host sets people free. Space Ghost isn't convinced, which prompts Zorak, in a girl wig, says, "Would I lie to you, sugar?" (and he continues to wear different wigs during the episode)
When Bobcat Goldthwait asks Space Ghost if he thinks that he's pretty, and in return says that Space Ghost is "kind of handsome too."
At the beginning of the Banjo episode, Zorak and Moltar are making small talk about soap and Zorak's new book. But the random subtitles make it seem like something completely different is happening.
Zorak: Moltar, look, I am green with evil. Moltar: Huh? Zorak: I said, did your mail order come in yet? Moltar: Yeah. Zorak: What did you get? Moltar: Soap. Zorak: Hm, what kind? Moltar: .... Lava. It's got pumice. Zorak: Yeah. Moltar: That your new book? Zorak: What? Moltar: I said, is that your new book? Zorak: Shut up, I'm reading my new book. Moltar: Sorry. Zorak: What? Moltar: I said, you can't read. Zorak: Yeah, yeah... Where's the Ghost? Moltar: In the back, with his new sea monkey kit.
Zorak: Moltar, I love you. Moltar: I love you too, Zorak. Zorak: We should get married. Moltar: Papa would never allow it. Zorak: But we're so in love... why not? Moltar: You know why. Zorak: It's because I'm an insect, isn't it? Moltar: Papa says... insects are bad folk. Zorak: I don't play fiddle. Moltar: I know, Honey, that's why I love you so. Zorak: What? Moltar: I said, I love you so. Zorak: Woe is me, for we cannot marry. Moltar: I am ashamed. Zorak: Do not be. Moltar: Let us elope in the night. Zorak: Yes!! You would do that for me? Moltar: No! Are you kidding! I will never marry the likes of mantis! You are a filthy beast! Get ye gone!
"Self Help": Before letting the guests out, Moltar asks for a kiss. This includes Rich Hall.
In the Christmas Special, when Zorak gets overly excited about the snow, Space Ghost tells him to calm down, come under the mistletoe, and give him a smooch. Cue pause.
When David Byrne was on the show, he seemed oddly uncomfortable with the thought of having a private talk with Space Ghost. What did he expect would happen?
For the entirety of the episode Urges, Zorak is more of less lusting after a guy in drag (true he doesn't realize this, but...).
The time where Terry Jones licked Space Ghost was odd enough. But then Zorak demanded to be licked too...
On the episode Lovesick, Space Ghost's girlfriend Ms. Nesbitt left him. Zorak tells him all about her new guy, with strangely intimate details, including that he's a great kisser (of course this is probably just Zorak being Zorak)
In one of the many parodies of the episode "Jacksonville," one of the common "twists" is to cut to one of the characters telling Space Ghost that they're pregnant. To add to the comedy, they're all men.
"Late Show": When Janeane Garofalo was asked who she would date, if she could date anyone, this was her response: "Catwoman and Pat Buchanan"
After blasting Bob Odenkirk several times (and him liking it), Bob says that he loves that he loves Space Ghost and begins to whimper and beg for the blasts.
On the episode Sphinx, after threatening to spank Harland Williams in front of everyone, Harland accuses Space Ghost of being naughty and quote, "liking wood."
Moltar's fanboying over Erik Estrada could be seen as a him having a bit of a mancrush.
Space Ghost: Moltar's got this Estrada problem. Zorak: Yeah, he wants to shake his hand and then pull it up to his mouth real quick so he can kiss it.
When John Henson told Zorak and Moltar that deep inside him is a big Slavic nurse, they demanded that he release her. His reponse: they don't have the money for that.
Terminal: When they brought in Dr. Drew Pinsky in order to diagnose if Space Ghost is really dying, Space Ghost seemed really admant about wanting to take his clothes off.
Space Ghost's fear and attitude towards Warren and Warren's obsession with Space Ghost all seems oddly akin to a situation where someone was taken advantage of by their mentor.
Zorak was so put off in the episode Chinatown when Moltar was traded away that he sang a song about it.
From "Waiting For Edward"
Space Ghost: [Shot of Space Ghost's head.] I guess my greatest fear would be to find myself hopelessly attracted to one of my coworkers. [Cut to show that Zorak is on his lap.] What are you doing? Zorak: That'll be ten dollars. Space Ghost: Get off! Zorak: [Leaps off.] You can owe me!
In "In Memory of Elizabeth Reed", when Moltar attempts to share some of his Star Trek fanfiction with William Shatner, Zorak points out that it isn't the same story that Moltar showed him earlier, and that Moltar's original story, "had naked men in it."
When Space Ghost gets drunk in "Idlewild South", at one point he straddles Zorak, kisses him (or presumably does, what with the limited animation) and declares that Zorak is now his girlfriend, "and they are going out twelve times."
This little exchange in the final TV episode:
Space Ghost: Moltar, reach down my pants and get the show budget to pay the bail. Moltar: No! Zorak: You know you want to. Moltar: ...I know.
On one of the webisodes, in order to drum up controversy to bring in viewers, Space Ghost orders Zorak and Moltar to kiss. They refuse, but not asserting that they don't swing that way. (which, in the webisodes, they totally could've gotten away with)
Space Ghost: Which of you is the straight man, and which is the wacky sidekick? Bob Odenkirk: Uh, he's straight and I'm gay. Wait, what did you ask?? Space Ghost: I said, which of you is the straight man, and which is the wacky sidekick? Bob Odenkirk: You're talking about, oh, comedy! Oh, shoot.