The main themes are that Zebra is very smart, the crocodiles are usually dumb, and often the crocs end up either killing themselves or otherwise failing spectacularly.
The comics can be appreciated more when you realize that almost certainly (but perhaps subconsciously on the artist's part), Zebra represents Israel and the crocodiles are Palestinian Arab terrorists.
Here is a recent series that demonstrates this (notice the punchline at the end):
The idea that the artist is passionately pro-Israel and anti-terror is apparent from this uncharacteristically somber strip from December of 2003:
Stephan Pastis, for his part, does not divulge any symbolic meaning to the crocs. But to my mind at least, the battle is remarkably consistent the Palestinian Arab war against Jews. Today's strip even includes the religious dimension of the terrorists:
Even if I'm wrong (and I don't think I am), it adds a bit to my enjoyment of the strip.
