Clerks still is his best film IMO. It had so much humor, insight, smart-ass lessons in life and low-budget charm. Mallrats had many of the same qualities but it just didn't go anywhere. Dogma just seemed too much like a Hollywood movie, it was trying too hard almost. And J&SBSB served it's purpose it end the series.
Clerks just had great execution of his ideas before he had the money and big Hollywood distractions that detracted from the storyline, I think he is a good storyteller when he's focused.