Code Geass has this increasingly through out the series. Nunally twice, Vileta once, Cornelia once and others. Kallen and Lelouch are, when captured, forced to wear strait jackets; CC has one as her ''daily clothing'. Also carried out by the soldiers involved in the Chinese uprising. Why were they carrying ballgags with them again?
In YuYu Hakusho, Kuwabara is tied and gagged in the Chapter Black arc in order for Sensui to use his Jigen-tou to slice through the dimensions- first with Toguro-ani's body working through Gourmet, then with a conventional rope and gag.
Akane from Ranma ˝ found herself in this predicament when Cologne tied her up and hid her in a storeroom, to keep her from interfering with Shampoo's plots. Surprisingly, even when Akane is more than capable of breaking free on her own, she refused to do so because Ranma was being a great big Jerkass. This is a persistently common trope in the series. Another incident involved Pantyhose Taro holding her as a hostage, and keeping her gagged and bound with (you guessed it) pantyhose.
No gagging involved, but in Strawberry Marshmallow, Miu called Nobue to tell her that Matsuri was her prisoner and was being tied up with a long rope. She demanded 5000 yen (a little less than US$50) or she would remove Matsuri's panties. Nobue went over to find... Miu tied up. Nobue took Miu's wallet, removed a 5000 yen note, and left over Miu's protests.
Tenma is captured, tied to a chair, and beaten by a dwarf Neo-Nazi crime lord in Monster. The scene is doubly valuable as a great demonstration of Heroic Spirit and Fanservice.
Hanaukyō Maid Tai La Verite episode 6. In the Baseball Episode the maid acting as an umpire is kidnapped (and shown tied up and gagged) and replaced with a Technology Department robot.
Ookami-san: Okami gets tied up by some school bullies in episode 2.
Happens to a few characters in Love Hina, thanks in part to Kanako being adept at this sort of thing.
Happens to often in Mnemosyne, Episode 1, Rin is strapped down and tortured by Sayara. Episode 3, Rin is bound to the handrails of sinking ship. Episode 6, Rin is chained to a table and ball-gagged in front of a chained Angel by Laura. Then there is Apos' torture victim in various episodes.
Happens quite a few times in the Pokémon anime, this. In the episode "Just Add Water", Misty is tied up with Dorian with tape across her mouth.
At one point in the RS arc of Pokémon Special, Flannery gets kidnapped by Team Aqua. She ends up with her hands tied to her back and with tape across her mouth.
Later on in Pokémon Special, during the BW arc, an undercover Grimsley ties up a Team Plasma grunt pretending to be a construction worker after knocking him out. He leaves the grunt behind to be punished, along with a comatose Black.
In Pokémon Origins, Mr. Fuju is bound at the wrists and ankles while taken hostage by Team Rocket.
Naruto gets tied up and gagged in one of the movies. As does Sasuke way back in Part 1, by Naruto, although he easily escapes.
This happens to Orihime twice in Bleach, although the first is only implied- Ulquiorra tells Orihime (who is upset because she believes one of her friends is dead) to eat. She refuses, so Ulquiorra tells her if she doesn't eat then he will strap her down and force it down her throat. We never see Orihime eat after that, so it's hard to tell if he followed up on this. Second time was with Grimmjow after he stole her out of her room to go heal Ichigo so Grimmjow could fight him properly.