In Yu-Gi-Oh! 5D's Tetsu Ushio has thick eyebrows in a permanent arch to underline his status as the overdramatic comic relief. José has a single, very long eyebrow. It covers even his eye.
Ushio in Yu-Gi-Oh! and several other early villains had these to make them look more threatening.
Amarao from FLCL takes this to ridiculous extremes with his prosthetic Oddly Visible Eyebrows, which is visually made out of digitally-rendered nori seaweed sheets. The fact that they're fakes only serves to emphasize his immaturity, as his actual eyebrows are very tiny.
Amarao also gives a pair to Naota to wear as protection. Of course, they don't last long.
Dorothy's eyebrows are seen by many fans as one of her defining traits, to the point of becoming a Running Gag; one official Yonkoma actually has her using them to imitate various Gundams' forehead crests, and there is at least one doujin where they turned into hands.
Lu Anon from Mobile Suit Gundam AGE has noticeably thicker eyebrows than most of the other characters in the series.
Souten Kouro features more than its share of Big Ol' Eyebrows. Especially noteworthy are Cao Cao's; it's not that they're all that thick, it's just that he has four of them.
Klan Klein in Macross Frontier is female, and when she's her natural 30 feet tall her eyebrows are normal, but when micronized down to her peculiar Sleep-Mode Size four-and-a-half feet, her eyebrows are relatively gigantic.
England, as they make him look more like a gentleman. His brothers share the eyebrows, and some of his colonies have them too. Australia and New Zealand have pairs as impressive as England's, and it's passed down to the Australian micronations (Hutt River and Wy) too. Hong Kong was supposedly cursed to get the brows.
Nonetheless, there are nations that have thick eyebrows yet are not linked to Britain: Cuba, Korea, Turkey, Greece, Ancient Rome, Denmark, Ecuador and sometimes Russia◊. India has noticeably thick eyebrows as well, but it's unknown whether it's an effect of him being a British colony or simply because he's Indian.
Mugi is an exceptional case of a girl with noticeable eyebrows, which apparently run in the family (although her eyebrows are more potato-wedge shaped than they are bushy...).
When Azusa imagines a more determined Yui, she imagines her with thick black eyebrows fixed in an angry position. In the background of her fantasy, the other members of the band each sport a pair as well.◊
In the 'Final' episode they're pickled radishes. At least, in Yui's fever-dream.
Sumi from Amaenaideyo!! also qualifies as another exceptional case of bushy eyebrows.
Ken Akamatsu was a big fan of this trope; many of the girls in his work have this feature, notably the "ideal" lead in A.I. Love You. Author Appeal, right there.
Asakura Ryoko, a tertiary character from Haruhi Suzumiya actually has noticeably larger eyebrows than the rest of the cast. This has not gone unnoticed by some artists and the results, well, see for yourself.◊
Damos in Pokémon: Arceus and the Jewel of Life has these, but he's a very strong man with Yami Yugi's voice, so it's okay. However, his descendant Sheena has the same eyebrows on a very pale, narrow face with otherwise dainty features... it looks pretty strange.
Yuki Yoshioka from Mitsudomoe has an extremely noticeable pair. Nobody really draws attention to them, but they draw more than enough attention to themselves.
The Puchuus from Excel Saga develop these when hit as well as an over-the-top angry Gonk face.
Those faces - and their eyebrows - are Golgo 13's.
While none of the characters you'd expect to see in such an over the top anime have big eyebrows, Code Geass gives us Kyoshiro Todoh◊, of all people, who seems to be the spiritual success or to Treize and Dorothy of Wing when it comes to the forked variation. Given, they're both Sunrise series... Charles, meanwhile, does not have overly huge ones, but impressive, nonetheless.
Blue Exorcist has Kamiki Izumo, whose nickname in-series (and among the fandom) is "Eyebrows". Amaimon also has them.
Miyamoto Musashi from Yaiba, whose eyebrows aren't only extremely thick but also longer than his body (it helps that he's very small).
Miho Jufuku from A Certain Scientific Railgun has these. After her boyfriend dumped her, saying her eyebrows were ugly, she decided to knock other girls out and do Face Doodling to give them eyebrows like hers. She seems to have fallen for Saten after Saten said her eyebrows were unique and cute.
Mai Minase of .hack//Liminality is another female example, though it's rarely mentioned in the OVAs.
Satsuki Kiryuin from Kill la Kill - or, as Ryuko refers to her, the "perpetually frowning, caterpillar-eyebrowed bitch." She inherited them from her mother Ragyo, who also has sizable eyebrows.
Iwao Kuroiwa has majestic eyebrows in Tokyo Ghoul, which accent his bug-eyed expressions. In the sequel, Takeomi Kuroiwa has his father's thick brows. It's the first hint of his identity, prior to his name being revealed.
In Otaku no Musume-san, this is a trait of protagonist Kouta Morisaki's family. The fact that Kanau has them too, is one of the factors that lead him to recognize her as his daughter when they first meet. Haruka's baby at the end of the series also has them.
in Mekko Rarekko Both Yamano Taishou and Fukami Youhei have very big eyebrows but Fukami has the biggest eyebrows in the series.