8-Bit Theater: Fighter supposedly used them on one occasion, but because of the art style of the comic, we don't actually see them. As he tried to use them on Black Mage, they didn't work.
Alien Dice gives us Swiftpaw, who has clearly mastered the trope. It helps that he's based on a fox.
Beyond the End: End has a tendency to break out the puppy dog eyes, just by his nature.
Carry On: Kathy can do these, but as Scooter puts it, "Somehow, "big Bambi eyes" just don't look authentic on a hyena."
Curtailed: Fox attempts this on Seley in this strip. Too bad Seley's immune.
The Cyantian Chronicles: Used effectively by Tae and Kea, the Akaelae Twins and ineffectively by Khaelis. Ironically, that's both literal and figurative Puppy Dog Eyes in both examples. Tae and Kea are wolves and Khaelis is a fox.
Dan and Mab's Furry Adventures: Jyrras Gianna generally employs these, helped in part by being the same age yet half the size of most of the cast. Lampshaded twice, in one strip where the other character is immune and in another where they are used on him (prompting a bemused "That's my gimmick!" when he recovers).
In this one, in which Sarah, intentionally or unintentionally, uses puppy dog eyes to make the principal allow her to wear a beret. In this one, Sarah does it to show off her general cuteness... err... that is, distract Susan... Yes.
Susan has finally used them too...inadvertently, when she learns that Justin doesn't have a version of her on his bridge crew in the Star Trek Online game. She's so surprised when told she's doing it that she feels her face to confirm it.
Grace managed to "convince" Ellen and Nanase to agree on a double date with her and Tedd.
Tedd, shocked by his own bout of badassery and in need of a hug.
In a subversion, Florence replies to an enormous terraforming robot's use of puppy dog eyes by saying, "Sorry. Puppy dog eyes only work when the eyes aren't bigger than my head."
Inevitably, Florence is ordered to use them at weapons-grade intensity. Being a canine, they work as designed.
Furry Experience: Used by Catand Dawn to get Ronnie's father to take them to a nice restaurant they both want to go to.
Anvil later uses her own set to convince Maxima to wear a thong on her not-date with Deus, though Maxima calls it creepy for an adult woman to pull it off.
Gunnerkrigg Court: It's not sure whether she's aware of it or not, but this page really accentuate Annie's eyes when she's apologizing.
L's Empire: Parodied. Carnation uses her eyes to hypnotize her brother Void (she uses her voice to hypnotize everyone else).
Monsters Can Be Heroes Too!: In "Jiggle", that's how Lime the Slime convinces Coal that she's a friend, when her previously dark eyes start sparkling and we get a zoomed in panel of them.
Spookybot: Because we're so immensely charming! Roko: No, that's definitely not it.
Sandra on the Rocks: Puppy-Dog Eyes have an unfortunate effect on Lavali in this strip, rendering her incapable of telling Aaina that Sandra isn't gay.
Saturday Morning Breakfast Cereal: Defied in "Cute", where a scientist doesn't want puppies to do this all the time regardless of their mental state and invents a way to make them look more like how they're actually feeling.
Katuses this, albeit sparingly, when she needs some help from her house-mate.
Kat herself is resistant but not immune to this effect.
The Silver Eye: This sort of pleading, pitiful look is described as the "orphan face".
Skin Horse: The cloying critters of the Whimsy Corporation pull this on Sweetheart — who is herself a dog.
Sleepless Domain: In a guest comic, Sally deploys these when asking Undine to give her and the others a ride with her Making a Splash powers. Undine, reluctantly, agrees.
Wapsi Square: This strip has Monica using puppy dog eyes to convince Darren to watch her dog while she's on vacation.
Tales of the Questor: Quentyn does it to get info from an elder. Apparently a pretty common technique among Racconan kits.
Two Guys and Guy: Played with when Guy's "puppy eyes" turn out to be a glare sufficient to intimidate the cop who just pulled her over for speeding.
"Lord Jesus! What breed of puppy is that? Hell-hound?"
Welcome to the Convenience Store: In this chapter, when a daughter is asking her dad to buy her a snack (when he only has enough money for said snack or his cigarettes). STA—ARE