A true second-price auction is one where the bidders (secretly) inform the auctioneer of the maximum price they'd be willing to pay, and the bidder who nominates the highest price wins, but pays the price nominated by the second-highest bidder. This is done in an attempt to eliminate the "winner's curse" and encourage the bidders to nominate their true maximum price. See http://en.wikipedia.org/wiki/Winner%27s_curse
eBay's proxy bidding system approximates a second-price auction because if everyone enters their true maximum, the person who nominates the highest value will pay (2nd-price + minimum-bid-increment).
In a sense they have that already, since eBay is a (quasi) second-price auction.