It stands for "a name that won't result in Microsoft's lawyers sending C&D's to Alex".

From Alex Russell: Actually, I was uncreative enough to name my last toolkit "netWindows" so this go-round we actually took a vote. Leonard Lin suggested "Dojo", and it won the vote. It doesn't really stand for anything.

We're different from closed source vendors because we appropriate random words out of *other* languages ;-)