Maya: Hamburgers (Mayoi liked noodle soup, which created a bit of a Dub-Induced Plot Hole in the fourth game.)
The difference in Maya/Mayoi's favorite food between regions is gently mocked in a yonkoma from the Official Casebookfan-manga collection, in which Maya remarks that she could really go for a burger, but she's forced to eat ramen as well "for the sake of Maya fans around the world".
Ema Skye: Karintou Snackoos. (Pictured. They make good projectiles too!)
Gumshoe: Instant noodles. (Though this has less to do with how much he likes it so much that it's some of the only food he can afford.)
Godot: Coffee. One of the rare cases where he appreciates the taste more than the caffeine (although he still despises decaf).
Truth in Television: People who appreciate coffee for the taste usually do prefer the regular kind. The decaffeinating process adversely affects the quality of the bean (long story short, the caffeine gets brewed out), so, all other factors being equal, a cup of decaf will always be inferior.
The heroine tells Sakuya that her favorite food is udon along the course of his route, in response to him asking her what she loves. Though the game itself begins with her telling Ryouta she can't sit still in class unless she's had some red meat, in Holiday Star she cheerfully tells Ryouta that she eats udon every day, only going without once every six months or so. He replies that she must not like it as much as he thought; he expected her udon-less days to be once every three years.
A Valentine's-equivalent holiday revolves around giving the bird of your affection the kind of seeds that they like.
The inhabitants of Mogeko Castle are obsessed with prosciutto. Yonaka can find packages of the stuff everywhere, and they actually have a religion based around it. Lord Prosciutto forgives the sins of all Mogeko, apparently.
Fleuret Blanc: Judge Grams really loves ginger, and by God so will you. Even FOIL's energy drinks are ginger flavored. This ties into a Stealth Pun: she has a soft spot for "gingers" — that is, redheads.