Can't say I've seen that. What's the point, if querying the card can return a statement saying not enough funds?
I'll let you know if I see a $0.01 deposit :P
They're checking the card is not going to be bounced by the card issuer, due to previous fraud, reported stolen, etc. By requesting payment of a nominal amount they're able to do an early validity check before their system accepts the card as valid for a larger payment.
It's not at all unusual, though sometimes it doesn't really achieve too much, as in this case.
Actually, I had a 'pre-auth' recently for a zero amount, even the issuer was kind of surprised to see that! Edited, Feb 21st 2012 8:16am by Kragorn