The ending part of "Bah Humduck" where Penelope kisses Pepe Under the Mistletoe was a rather sweet moment.
Sweet, and a little funny, considering one would expect her to run...Nope. She grabs him, flashes a flirty look as he looks shocked—like even he expected her to run—then gives him the make-out of his life.
"Past Perfumance" shows that even when Pepe finds out that Penelope isn't a skunk he still likes her, and paints his stripe black so he can resemble a cat.
Used similarly in "Scent-imental For You", after a hairless dog removes her skunk disguise (in reality a bad attempt at a fake pelt), Pepe reveals his own disguise and to in fact be a dog himself. The lonely dog hugs Pepe smitten, while Pepe reveals a second disguise covering his normal skunk self to the audience.
The Valentine's Day commercial was a pretty sweet moment as well. The premise of the Pepe shorts was that Penelope would somehow get a white stripe down her back and try to avoid Pepe for the rest of the short. In the commercial, Penelope was voluntarily painting a white stripe down her back because she liked being with Pepe. The fact that the commercial also implies they're now an Official Couple is pretty squee-inducing for any Pepe/Penelope fan.