A bit of speculation on my part.
The Third Kryptonian is from one of the 52 Earths, and is a female version of Superman.
How about a female version of SuperBOY?
Here's what I posted on another message board regarding the same question:
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On another thread covering this very same question, one poster suggested it was
Supergrrrl , who appeared in the "Hyper-Tension!" arc of
Superboy (Issues #60-65). This could be a real possibility for a couple reasons.
First, Supergrrrl comes from the
Elseworld's Finest: Supergirl and Batgirl universe. This alternate Earth has proven popular with fans (DC Direct made figures of both Kara and Babs), and it's likely to be one of the 52.
At the conclusion of "Hyper-Tension!", all the Superboys were returned to their native worlds. But it's certainly possible that some got sidetracked, and there was only one female "Superboy". Perhaps Supergrrrl's uniqueness caused problems on the way home? After all, she's not a clone of Kal-El (or a younger Kal-El), but a clone of Kara Zor-El...
Oh, dear -- I just realized this. We already have TWO Karas (Power Girl and the new Supergirl). Add the clone of an Elseworld's Kara Zor-El, and we'll have THREE counterparts of the SAME person inhabiting ONE universe! No wonder the Third Kryptonian has got to go!
You can see Supergrrrl's debut here:
http://community.livejournal.com/scans_daily/2703079.html(Frankly, she STILL looks better in that jacket than Kon-El ever did!)