Honestly, I feel like my favorite varies on how I feel/what I am watching at the time.
Mallrats holds a special place for me since it is what hooked me first. Then I saw Clerks and Chasing Amy, with Dogma later being the first I saw in theaters. Chasing Amy may be the actual best, though. I don't know. Like I said, it's hard to decide. Jay & Silent Bob also felt like a huge event for me, and was so much fun.
I would say, though, that while I really like it, Clerks 2 would be my least favorite (but still better than most movies).
I also need to acknowledge how much I love the Clerks cartoon. That thing is great.