I've been rewatching a lot of clips on YouTube. It's a great comfort show. The chemistry between Charlie, Alan, and Jake was incredible. And the side characters (Berta, Evelyn, some of the girlfriends) really added to it.
It's hard to say what the best episode is because there are a lot of great ones, but some of them include:
-The one where Jake stays with Charlie and Alan for the week and he gets left behind at soccer practice
-Alan's old friend comes to visit and she tells him and Charlie that they'll never get to be with her ("NEVER, NEVER, NEVER!")
-The one where Alan falls off the ladder and Charlie has to take care of Jake for the weekend
-Jake has to write a book report, but he keeps losing the book ("FIND....THE.....BOOK!")
For about five or six years, the show was consistently funny. The first season without Charlie wasn't that bad, but they turned it into a cartoon afterwards. Charlie brought a certain kind of magic to the show that they couldn't replace.