Season 1''s "Just a Guy" was pretty funny, especially with Sonic's happy place.
Season 2's "Mister Eggman" is also pretty good.
I like all the episodes that I chose to create a transcript of, in which most of them can be found here. My favourite two from both seasons are "Two Good to Be True" and "Lair On Lockdown", although "Three Men and My Baby" is right up there as well.
What do you think?