I've been having a few theories as to what may go into this port.
The more obvious theory I've been investigating it the fact that Serial Port 2 is really small. There was some talk a while back about those micro hard drives that IBM was cooking up, and though those are more like the size of a coin, versions that could fit in that bay under the GameCube are possible. This would sort of like the HD solution that the Xbox has, or the huge memory card solution that the PS2 has, or perhaps even an Expansion Pak type deal from the N64. One thing's for sure, whatever it is, it's going to be flush with the bottom of the GameCube once it's installed, since the Game Boy Player takes up the whole rest of the space on the bottom. (The opening on the side would probably be used for getting a grip on the thing to take it out.)
This is why my second theory is starting to make more sense. Look at the opening on the side of the GameCube where Serial 2 opens on the left side. It's different than the two ports on the right side, as they are square-shaped and this one is small and semi-circular. As you can see from a
revealing shot from this side with the GB Player attached, there's absoultely no room whatsoever for a plug to fit into that space comfortably. It just so happens that this is the same side that has the "storage area" door.
What I'm thinking may be possible is that Serial Port 2 isn't for a small device, but rather, just a connection for a another hardware expansion, ala the Sega CD, 32X, 64DD, etc, but having it docked next to the GC, rather than under it. Nintendo always wants to leave the doors open for doing this, and the other two hardware pieces they've released haven't done that as of yet. Now, the big problem with this idea is that the intake vent and fan are on this side, but there's nothing that says it won't be something of a loose, cable-attached device for the system, such as a camera, mat, light gun, or something of that sort.
Of course, there's the age-old theory that it will go unused, which was one of the first things I thought when I saw the underbelly of the GameCube for the first time, but considering that Nintendo has two of those three ports used after only 15 months of the GameCube's retail life, there's still plenty of time to use it.