Theodore has trouble standing up for himself. The episode "Dave's Wonderful Life" shows that he used to be shy and would have become a hermit without Dave's influence.
For the Chipettes, Jeanette. She is actually more like Theodore than Simon in a sense, as they are both sweet, timid, and shy.
Male example: Shifty Dingo in the 2nd season of Blinky Bill after his Heel–Face Turn easily qualifies as one of these. He's much more quiet than the rest of the gang and also has a Lovable Coward side to him.
Stacy from Daria, the shy and sweetest member of Quinn's Fashion Club.
Doug Funnie, the title character of Doug, is a more subtle male example. However, it usually depends on the episode.
Another male (kinda) example from Futurama would be Kif Kroker, who is usually a Deadpan Snarker when dealing with his boss ZappBrannigan, but seems to show this side when his Love Interest Amy is around. In the episode that brought them together as a couple, she kept getting phone calls of someone breathing and panting heavily on the other end; she assumed they were prank calls, when it was really Kif calling to tell her how he feels, but too scared to say anything, thus hyperventilating until he hung up.
Along with Kif, there's Mom's second eldest son, Larry. Who is a spineless, Nervous Wreck and finds it difficult to even say aloud words like "bra".
PJ from Goof Troop is a rare male variation: He's way too shy to make friends with anyone other than Max (who opened up to him first), and Bobby in the movies (who seemed to meet him through Max). He's highly timid around everyone else, including (or perhaps especially) his own father. When he got a crush on a girl in his class they were Twice Shy. This is played entirely sympathetically, and often seems to be trying to make him pathetic enough that the audience doesn't think of Pete as a Designated Monkey. In the second movie, he gets a Love Interest... because she asks him out. Then this trope disappears.
Eugly the rabbit from Kaeloo is a shy but extremely sweet girl who barely says anything.
Coco Pommel, the Beleaguered Assistant to the Jerkass-ish Suri Polomare, is incredibly submissive to her boss as she's forced to do all her dirty work and get her coffee. At the end of the episode she appears in, Coco musters up the will to quit her job.
Cheese Sandwich, the only pony who can give Pinkie Pie a run for her money in terms of Fun Ponified, and the pony equivalent of "Weird Al" Yankovic, admits to being painfully shy when he was a colt. It was around that time that he met Pinkie and was inspired to make a name for himself as the craziest party pony in Equestria. Even then, he still travels Equestria with only his rubber chicken as a companion.
Marble Pie, Pinkie's sister, perhaps even more than Fluttershy. She had a mane style that forms a bang over one eye she visible hides behind, runs away when she is introduced to Applejack's family, and her only dialog are muffled "mmm-hmms". That said, when Pinkie pairs her with Big Macintosh for various events, she clearly opens up just a bit to a fellow Shrinking Violet.
Filburt from Rocko's Modern Life. He's even a turtle (as well as being named after a nut) with a literal shell to go along with it, which he will often retreat into in times of social stress. In one episode, he manages to get past this and become a lounge singer, although not without first feeling incredibly self-conscious even that Rocko heard him singing in his own trailer, and suffering from a very intense amount of stage fright. He does eventually get a Love Interest, though when he plans to propose to her she succeeds in proposing to him first.
Schoolhouse Rock has an example in Mr. Morton (the subject of the sentence; and what the predicate says he does) who is played entirely sympathetically. His entire song is about how he's trying to get his neighbor, Pearl, to like him but is way too scared to ask her out or even talk to her, including two lines that explicitly state "Mr. Morton was very shy" and "Mr. Morton was very nervous". Eventually, she ends up proposing to him, and they live Happily Ever After.
A rare male, yet non-Butt Monkey example: Austin from The Backyardigans also embodies this trope. Not only he's purple (violet), during season 1 he was very shy and didn't speak a lot (he had songs about that). Over the course of the series, he becomes more outgoing and gets dynamic lead roles.
The Funny Company, a syndicated series from the early 1960s, featured a girl named Violet who really did shrink down to doll size when she felt self-conscious.
Flora from Winx Club. While not that reserved, she was very shy when she had a crush on Helia and was reluctant to confess her feelings.