When discussing plans for after High School, Fred implies that he and Shaggy will be rooming together, but actually asks if Shaggy prefers cotton or linen bedsheets.
When Scooby realizes that Shaggy's relationship with Velma is serious, he acts just like a jilted lover.
Scooby: Are you... cheating on me?
And when Scooby and Shaggy are too caught up in a happy reunion to run from a Killer Robot dog, Velma tells them "Let's go, lovebirds."
Fred's dad's old fraternity Mu Gamma Tau only seem to be interested in working out and wrestling... a lot.
In episode 4, Rung Ladderton and Fred comment on each other's ascots... and then swap saying how good they look on each other.
In episode 3, Velma appreciatively looks Daphne over when Daphne changes into a bikini. Daphne then asks her to rub sunblock on her back. Note that Velma is often already thought of as a lesbian in Fanon.
Daphne gets some with Thorn of the Hex Girls in "In Fear of the Phantom".
Thorn: I'm a good look for you, Daphne.
"Mystery Solvers Club State Finals": Principal Quinlan and Angel. While they're alone (with Speed Buggy), Quinlan awkwardly compliments Angel's muscles, noting that they're bulky like female wrestlers, except less vein-y. Later, Angel encourages her to do CPR on Speed Buggy, after which Quinlan becomes Hotter and Sexier.
"Where Walks Aphrodite": When Aphrodite casts her love spell, everyone seems to fall for a member of the opposite sex...except Mayor Jones and Sheriff Stone, who are seen dancing together in the streets. Not to mention all the little dates they seem to go on throughout the show...
There's an undeniable Les Yay element between Velma and Amy the mermaid in "The Siren's Song."
Velma: She's my special secret friend, so don't any of you think about stealing her! [beat] That was awkward.
At the end of the episode, Velma is heartbroken to see Amy with legs... and also kissing a man.
Episode 22 gives us Dr. Rick Spartan and his assistant Charles/Cachinga. They argue like an old married couple, but the minute Rick is seriously injured, Charles is rushing to his side, worried sick. Of course, Rick is married and his wife's love for him is the reason she dressed up like the Headless Horror to begin with, to try to convince him to live a normal, non-adventuring life, but it only plays down the Ho Yay a little. By "The Devouring", Marion has actually left Rick, presumably due to his adventuring lifestyle, but one can speculate.
Episode 24: Night Ranger collects magazines with men in what Daphne calls "mankinis."
The first season had open animosity between Velma and Hotdog Water. The stated reason was because they were simply scientific rivals, though many fans interpreted it as a Foe Yay situation. By season two the writers seem to have adopted this theory, or at least deliberately played with it. The two have gone from rivals to partners and friends.... really, really close friends. The most obvious sign is that, when Hotdog Water replaces Daphne briefly in the opening sequence, she's seen cuddling a photograph of Velma. To say nothing of her last appearance and line in the series: "That's my girl."
"The Hodag of Horror" features a disgruntled Fred who complains about being labeled 'Scarf Boy' by Velma. If her codename of 'Smart Chick' is anything to go by, she chose all the codenames...including Daphne's codename of 'Smoking Hottie.'
Season 2 also gives us Ricky and Pericles' relationship. Pericles even seems to quite literally want Cassidy Williams to Die for Our Ship! It doesn't help that by the time "The Devouring" happens Pericles has pretty much gone abusive boyfriend on Ricky, smacking him around and telling him he's only there to serve him.
Episode 45: Scooby and Shaggy go on an eating binge to chase away a gluttonous demon; they tuck into a giant cake at each end and end up kissing each other-on the lips!
The current Mystery Incorporated is the latest in a long line of mystery-solving crews with a Talking Animal. Most of them have two men and two women. At least two of the people in each mystery solving gang end up together. We see pictures of them in the episode "Night Terrors." However, there's a group of monks, which could be easily dismissed since they're Catholic monks, but there's also a group of all girls. Make of that what you will...
In "The Wild Brood", Fred tells Odnarb that he can call him "Fred" or "Freddie", but he can only call him the latter if they're dating (because that's Daphne's Affectionate Nickname for him). Now keep in mind, Scooby called him "Freddie" in "In Fear of the Phantom", and Velma calls him "Freddie" in "The Menace of the Manticore" and Shaggy also calls him "Freddie" in "All Fear the Freak"...