Jeff Daniels is Bernard, a novelist who has enjoyed great success in the past, but now finds it hard to sell his work. He is the textbook definition of an intellectual snob. His character is pretty much summed up in one of his first lines. After his son tells him that they're supposed to read Nicholas Nickleby in class, he responds with a flippant shrug, saying "Minor Dickens." He seems disappointed with almost everything, he's impressed by nothing, and he seems to think that his tastes are the only ones that matter.
Jesse Eisenberg is Walt, the son whose class is reading "minor Dickens." He's 17 (I think) and he's already becoming a clone of his father. During the Nickleby conversation, his mother tells him maybe he should read it himself and see what he thinks, he responds with "I don't want to waste my time." He criticizes his girlfriend for having too many freckles on her face, and believes he can "do better." It's fun to see him fumble, though, such as when he tries to impress his girlfriend by describing The Metamorphosis as "Kafka-esque."
Laura Linney is Joan, Bernard's wife and a fledgling author who is trying to step out from her husband's shadow. Naturally, Bernard being who he is, he tries to make her doubt herself, but thankfully living with him for almost twenty years has not made her lose her ability to think for herself. She has her foibles and has made a lot of mistakes, but she truly loves her sons and feels sorry for Bernard's self-inflicted misery.
Owen Kline (son of Kevin Kline and Phoebe Cates) is Frank, a self-proclaimed "philistine" at 11 years old and Bernard and Joan's other son. He wants to become a pro tennis player, but Bernard wants him to realize that he'll never be a McEnroe so there's no point in trying. Frank is also discovering the joys of puberty and the nectar of beer and hard liquor.
The Squid and the Whale is very much a character mosaic - lots of richly detailed writing and multi-layered performances. It's apparently based on the writer/director's own experience with his parents' divorce, and I think that really comes through. These seem like real people. People we all know. Speaking for myself, I've met lots of Bernards and Walts just in the time I've spent in the Harry Potter fandom. This is one of those movies that focuses on relationships between the characters more than the plot. It ends fairly ambiguously, but you've met lots of interesting people along the way. All of the cast is superb, but I think perhaps especially Jesse Eisenberg. Laura Linney's Joan is my favorite character, though.