Wonder Woman, and no wonder (pun not intended, at least not consciously): Her creator may have been into bondage himself, but he definitely wrote it into the job description. The original Wonder Woman has superhuman abilities... unless her vambraces were welded together by a man, at which point she became de-powered. So you can expect incredible amounts of bondage throughout the first couple decades of her comic, especially given that she nearly constantly allows herself to be captured in order to be a Play-Along Prisoner. It's such a common occurrence - to the point of once suggesting that the villains threaten to untie her - that the Superdickery website has an entire gallery devoted to it. Steve Trevor tended to end up captured and tied up pretty often as well, and unlike his girlfriend could not just snap the ropes and/or chains when he wanted to leave.
The villain the Mask gets her name from the poisoned S&M style mask/gag combinations she locks her victims in.
Wonder Woman (1987): Kimberly Dunn gets gagged and tied to a chair by Doctor Psycho disguised as Veronica Cale's pet enforcer. Then Cale shows up and rants at her before murdering her. Later on Cale gets a taste of her own poison when Doctor Psycho ties her up and gags her and tosses her in a closet.
D-List Superheroine Empowered ends up like this so often that villains, innocent bystanders, and her own teammates regard her as a laughingstock and she occasionally points out the shortcomings of gag design to the mellowermooks. (Very heavy on the fetish fuel, this series. In fact, it's part of its origin.)
Disney Comics at one point has the Beagle Boys demonstrate their convenient king-size Coil O'Rope that they carry around simply to tie up Donald Duck or Scrooge or whoever is opposing them on their nefarious plans.
In Red Daughter of Krypton, in order to transport an out-of-her-mind Supergirl safely, a group of Green Lanterns gagged and chained Kara with solid light constructs and placed her inside a containment cell.
Bizarro tied and gagged Bizarrogirl before getting her into the rocket which would take her to Earth.
Kara also ties up and gags Bizarrogirl before flying her back to Bizarro World.
Captain Marvel is a well-known male example; Billy's always bound and gagged because he has to speak his magic word to become Captain Marvel. Naturally, this also happened to his sister, Mary Marvel, as well as Freddy Freeman AKA Captain Marvel Jr. for the same reason. Also, their occasional teammate Kid Eternity, who has to speak his magic word to summon a historical or mythological hero.
The Adventures of Tintin - Tintin has been tied up on several occasions and, in one case, gagged, but has never been tied up and gagged at the same time. In fact this happens inevitably to somebody or other in just about every adventure (Captain Haddock, Professor Calculus, Nestor, and a slew of bad guys).
The first volume of Spider-Woman also features quite a bunch of tie up scenes of Jessica Drew, and at least there's one scene where she's also gagged.
Nightwing Dick Grayson gets tied up a lot, to the point that one of his villains had the ability to manipulate cloth in order to tie him up as her superpower.
At one point in Robin Stephanie underestimates Czonka and ends up tied up and gagged in a rigged to be demolished project. When Tim finds the clues which led her there he makes the same mistake and goes to untie her without first making sure of where Czonka is and gets knocked out and tied up and gagged for his troubles.
Nyoka the Jungle Girl is filled with this. All over the place. Nyoka gets tied up by bad guys all the time, many different ways.
Justified for many of the Marvel Universe magic users (Doctor Strange, Scarlet Witch, Wiccan, etc.), who need the free use of their hands and voices to cast spells. Some of them have learned the basics of self defense (Strange is a full-fledged Kung-Fu Wizard) so they can protect themselves.
In Violine, Violine reads the mind of her rescuer and sees herself like this, clueing her in to his true intentions, and quickly fights him off, to the point of crashing his car. Later actually happens in Muller's dungeon, providing the image for Torture Cellar. Even her mouse gets tied up. Redder also ended up like this in a flashback.
Harley Quinn: her most recent comic books in the New 52 series has had a heavy emphasis on ballgags, with her using one to gag a victim at least once per issue as they have progressed. Harley herself was bound and gagged in the first issue of Harley Quinn and Her Gang of Harleys.
There are plenty of instances of characters getting tied up on both sides in Injustice: Gods Among Us. Within the first few chapters, Harley Quinn is captured by Green Arrow to protect her from Superman, and it only goes downhill from there,
By the final issues of Spider-Verse, all three of the special totems are captured by the Inheritors.