Trompez L'esprit

Trompez L'esprit (French for Illusions of the Mind) is a Foster's Home for Imaginary Friends fan webcomic created by Deviant ART user Pentical. It takes place several years after the original show, where life for imaginary friends hasn't exactly gotten brighter. All imaginary friends are now under heavy supervision and are required to be chipped by their owners, those who aren't are taken in by the newly-formed Bureau for Imaginary Control. The BIC began their rampage with Foster's, claiming the house needed to be put under quarantine and taking many imaginary friends and even Frankie into custody. Despite fighting back, very few were left, and those who were (Mac, Bloo, Mr. Herriman, Madame Foster, and a small handful of imaginary friends) were forced to hide out in a bomb shelter for the next several years.

The main protagonist is Kate, a young imaginary friend who has been suffering the same dream over and over again. Not only that, she also notices she's not quite like the other imaginary friends, as she grows and matures like a human child and doesn't remember her creator. After Mr. Herriman, while lecturing her, accidentally slips up and nearly reveals a well-hidden secret, Kate becomes convinced there's something more to her than the others are letting her in on, and she begins asking questions and investigating. Seeing how much it is upsetting her, Mac, who is now a young man, finally reveals the truth of her past, that she is actually the half-human daughter of Wilt and Frankie, and the BIC was after her specifically. Desperate for more answers, Kate, along with Mac and Boo, sets out into the real world, but things don't go as simply as they may have hoped and they end up on the run from the BIC with even more questions than before. Later on Jake Derbihill, a detective, and Betsy, another imaginary friend join the trio. Together, the group searches for answers about Kate's past and the friends who were taken by the BIC.

Can be read here. Unfortunately, it hasn't been updated since 2009 and may very well be considered an Orphaned Series by this point.

Tropes used in Trompez L'esprit include:

Animesque: Sort of. The manga influence is there, but it still retains a bit of the Western cartoony style the original series had.
Art Evolution: Pentical's drawings become more detailed in the later comics.
Bland-Name Product: Many, such as the search engine "Moogle" and a restaurant called "House of Waffles"
Breaking the Fourth Wall: Occasionally characters are shown either being crushed by or staring at the speech bubbles.
Crapsack World: For imaginary friends and occasionally their sympathizers, at least.
Cross-Popping Veins: Used sometimes.
Darker and Edgier: Somewhat.
Dead Fic: Most likely, it hasn't been updated since 2009.
Donut Mess with a Cop: The cops are shown eating donuts in chapter 4.
Face Heel Turn: Dr. Geisel appears to have pulled this at first, but it turns out to be an imposter named Maynard Geirfrie. The real Dr. Geisel apparently died six years earlier.
Face Palm: Mac does this quite a bit. Mostly in response to whatever Bloo says.
Foreign Language Title
Half-Human Hybrid: Kate is half human, half imaginary. To be even more specific, she's the daughter of Wilt and Frankie.
He's All Grown Up: Mac.
Human Mom, Nonhuman Dad
It's All My Fault: Part of the reason why no one tells Kate of her past for so long is because Mac was afraid she would blame herself for all the awful things that had happened. It ends up being Subverted though, as Kate is aware she was too young for it to be her fault and she would have gotten over any guilt eventually.
Jerk with a Heart of Gold: Bloo is still Bloo, but he genuinely cares about Kate and Mac.
Orphaned Series
Papa Wolf: There's no way in hell Wilt's gonna let the BIC take his daughter.
Parental Abandonment: Both Mac and Kate.
Peek-a-Bangs: Sort of. Kate doesn't actually have hair, but she does have pointy cheeks, which seem to act as hair and occasionally cover her left eye.
The Reveal: That Kate is half-human. It's not particularly shocking though, as it's hinted at throughout most of chapter 1.
Sweat Drop: Like the Cross-Popping Veins, it's used occasionally
Wall of Text: Played for laughs in chapter 1, where Mr. Herriman is actually being weighed down by Kate's speech bubble as she rants.
Webcomic Time: The comic spanned between 2005-2009, but no more than a few weeks pass in-story.
You Remind Me of X: Kate apparently reminds Mr. Herriman of Frankie quite a bit. Make's sense, she is her mother after all.