In the episode "Duck Blind" Darkwing says that he sent Megavolt to the electric chair twice.
In "Just Us Justice Ducks", Darkwing says to Morgana, "Let's get amourous." And remember, this show wasn't even on cable, unlike the other show that made that joke.
Also in the episode "Ghoul Of My Dreams", when Darkwing is investigating Morgana and enamored by her beauty, he says "But you're the prime seduction....I mean suspect!"
That episode had more sexual tension than usual with DW obviously having erotic dreams about Morgana as a giant and her later kissing him so passionately that a very deep, booming voice is heard from within him saying "Oh yeah"
And in the episode "U.F.Foe", Darkwing puts his hands on Gosalyn's ears when he hears Launchpad is going to oompa with Tia, and warns them to watch their language. Launchpad quickly explains that the word means "marry".
Also in the episode "Duck Blind", Megavolt tells Darkwing that he's tired of him busting his bulbs.
"Clash Reunion" has Drakey "The Dweeb" Mallard in high school accusing the Jerk Jock Ham String of stealing a pencil to "keep score" of... he doesn't say what, exactly. It might be Ham's football games, but he does also have his girlfriend Prina Lott with whom he was about to do some kissing when Drake cut in between them to make his accusation.
In "Paint Misbehavin'", when Splatter Phoenix suffers Clothing Damage after her minions mistakenly attack her, one of the tears on her shirt is in the breast area.
"My Valentine Ghoul" has both Darkwing and Gosalyn fall in love with Negaduck after they are affected by the love potion. While their love for Negaduck is played more like a platonic love, there is still some Homoerotic Subtext from the love struck Darkwing and Gosalyn's attraction to Negaduck becomes rather squicky when you consider that 1, she is underage, and 2, Negaduck is the evil twin of her adoptive father.
Issue #2 of the comic, when Darkwing sees the Crimebots being upgraded with accessories.
Darkwing: Now all those orders I filed for chains and cowboy hats make sense! All this time I thought someone had a unique way of enjoying the weekend.
It's no longer there in the Joe Books omnibus, though.
Happens literally in Issue #3 of the comic when Megavolt says "I bet he had a crappy office job all this time!" in reference to Darkwing.
This is no longer the case in the Joe Books omnibus, as it rephrases the sentence and replaces "crappy" with "crummy".
Issue #5 has reporter Dip Dopson say that he wouldn't mind kissing Darkwing on the mouth. A background character listening to the radio broadcast even mentions that it is a weird thing for a radioman to say. Funny thing is, unlike the above instances, this wasn't edited out of the Joe Books omnibus.
In the twelfth issue, Duckthulhu alludes to red and white wine. This one also remained unchanged in the Joe Books collection.
in the fourth issue of the Joe Books revival, Darkwing uses a magazine with a centerfold of an electronic device to get Megavolt to help him defeat the Gnatmare. Just in case Megavolt's reaction to the magazine doesn't make it clear that it is a stand-in for porn, Launchpad is even seen covering Gosalyn's eyes when the centerfold is first seen.