Like first base, second base is often manned by former shortstop prospects converted late in their minor league careers over to second base. Usually, the ones moved there have weaker arms that play better at second than at short. As such, you'll very rarely see the very best prospects at second until they're close to the majors, or the player gets moved after a couple of years where they start to struggle with their range.
Given this, there's a remarkable lack of upper level second base prospects out there right now, after having seen Dustin Pedroia graduate to the majors last year. Most of the other prospects are older, such as new Royal Alberto Callaspo.
1. Asdrubal Cabrera, Indians, 11/13/1985, 22
The first choice is not difficult at all. If I had to pick between Dustin Pedroia and Asdrubal Cabrera before the 2007 season, I'd have taken Cabrera. Pedroia's 2007 stats with Boston were not projected at all. He performed better in the majors with Boston than he did in AAA Pawtucket the year prior. Ah, the joys of the green monster (Pedroia had a .912 ops at home, .729 ops on the road -- largely due to the 11 extra doubles hit at Fenway which would be fly outs elsewhere). Assuming I'm building a team that will play its games outside of a park with a giant formerly green monster in left field, I'd still pick Cabrera over Pedroia.
On that same note, it appears, at least so far, that Jacobs (err, I mean sellout, err, no, wait, Progressive) field doesn't suit Cabrera so well. Cabrera's splits are the opposite of Pedroia's: .710 at home, .828 on the road. The sample size is pretty small though, so let's see what happens next year.
ML Stats: 159 AB .283/.354/.421 101 OPS+
2. Tony Thomas, Cubs, 7/10/1986, 21
Thomas is one of those rarest of players, a guy who's a prospect as a 2nd baseman. Alas, that also means that he's just average at the position. I think there's hope there though. He's got tremendous speed, having swiped 28 bases on 30 attempts. He just needs to turn that speed into range. With his bat, you can bet that the Cubs will try everything they can to get him to improve defensively. Speaking of his bat, there's really nothing negative to say there. He's got good plate discipline, fast hands, and good power. He should be the Cubs starting second baseman in 2-3 years.
SS Stats: .308/.404/.544 28 SB, 2 CS
3. Damon Sublett, Yankees, 9/22/1985, 22
This pick is more about the lack of prospects at the position than as strong of an endorsement of Sublett as it seems. Don't get me wrong, Sublett's a nice prospect, but he's certainly blocked in the Yankees system in favor of Robinson Cano. Plus, he played in short season Staten Island last year, and at 21 he is expected to perform well at that level. He's just average defensively, but he's good enough to stick at second.
That said, he had the second best OPS among second basemen in the minors last year (#1 was Jared Goedert, an Indians prospect now stuck behind Cabrera above--but who has a hurt shoulder and just moved to the position at the end of last season, so there's no way to know if he can stick there). He's shown good potential, and probably will end up as a utility guy in the majors.
SS Stats: 239 AB, .326/.426/.531 10 SB, 4 CS