In the Street Fighter series, especially earlier on, Ryu and Ken possessed excessively large eyebrows, apparently made from M. Bison, Balrog, and Guile's missing eyebrows. Ryu's are so big at times that they overlap his headband.
The Japanese releases of Ratchet & Clank games gives Ratchet very thick, bushy eyebrows that many American fans refer to as "woolly bear caterpillars" - his eyebrows are fairly thick in the American version as well, but the Japanese release specifically stated he was given thicker eyebrows "so fanartists would have a place to start drawing from."
This seems to run in the Mishima Family. Jin's and Kazuya's are impressive, but somewhat less than grandpa Heihachi's. The Spoony One spoofed this in his review of the anime and live-action Tekken movies by wearing progressively larger construction paper eyebrows.
Piston Honda of Punch-Out!! has giant eyebrows that have their own sound effect. He twitches them before he punches, which is your cue to dent his face.
Lord Gongora from Lost Odyssey has extremely bushy eyebrows. His unwilling lackey Jansen even refers to him as 'Lord Eyebrows'.
Yukari Yakumo from Touhou normally has average eyebrows, but gets subjected to this trope in the works of doujinshi circle Hot Dog Chuck.
Cirno now gains an official one with Touhou 12.8.
Princess Suzushiro Shikikagura from Princess Waltz sports a pair prominent enough to earn an extra look and a nickname ("Eyebrows Girl") from Liliana.
K.K. Slider from the Animal Crossing games has some powerful brows. Better yet, they're based on a real guy.
Winfred "Big Wins" Kitaki from Apollo Justice Ace Attorney has his eyes covered by his insanely thick eyebrows until the end of the trial. His eyes are revealed to be tiny and insatiably cute. Kind of a subversion really, since before that, you're meant to think his eyebrows were his deeply-sunken eyes, making Winfred look insanely scary.
Ganondorf of the Zelda series sports a particularly magnificent pair of eyebrows that are not only bushy, but actually extend back to join with his hair.
Ralph in The Legend of Zelda: Oracle Games has forked eyebrows, though you don't really see them in-game. So does Queen Ambi, though again, you have to look at character art to see them.