Hear! Here! I have had the same question.

Hear! Hear! appears to be a shortened form of "Hear ye! Hear ye!"

And Here! Here! looks as though the speaker is trying to rope in the attention of a distracted and even disagreeable audience.

I'll cast my vote for "Hear! Hear!" but it's easy to imagine how "Here! Here!" would make sense, too. (This reminds me of what's going on over on the XXXXX and OOOOO thread. Lots may be rationalized when drawing viewpoints. We'll see what Mr. Ed has to say.)