Season 1>season 3>season 2>the rest(but seasons 4-5>6-13)
I think that many of season 1 episodes were about their great friendship: Bubblestand, Naughty Nautical Neighbors, Home Sweet Pineapple, Hall Monitor, Sandy's Rocket, Texas, Nature Pants, Opposite Day and so on and so forth.
Season 3 is a bit better than season 2 in term of their friendship because it has some more good episodes for this: Chocolate With Nuts, Wet Painters, Club Spongebob, Snowball Effect, New Student Starfish, Mid-Life Crustacean, etc.