The list is top prospects, period; however, the guys up toward the top are probably more likely to make an impact this year or next, simply because they're easier to project than any other players. When you have a player who played one season of low A-ball, chances are you won't be able to get an accurate idea of what he's going to do.
As for Baseball Prospectus, you can check out their book, or check out some of their free stuff over at http://www.baseballprospectus.com
There's a lot of discussion regarding these prospects, but it's all in the Premium articles, so I can't post full articles. But here are a few exerpts:
Top 50 - Outfielders wrote:RJ: Who ought to rank higher: Francoeur, with his overall tools and defensive ability but no plate discipline, or Jeremy Hermida (Marlins), who knows how to walk but doesn't have much power yet (although it appears to be slowly developing)? I don't have strong feelings either way.
NS: Francoeur versus Hermida:
PECOTA will generally prefer a prospect with good power but no plate discipline to a player with good plate discipline but no power.
Players with good power tend naturally to develop somewhat acceptable walk rates, as pitchers will throw around them more often. The opposite effect is somewhat true: players with good batting eyes will tend to work themselves into better hitters' counts, and thus develop more power. On the other hand, these hitters will be challenged more frequently as they move up the ladder, and the pitchers can throw the ball by them more effectively.
It's a fairly complicated sort of interaction. One thing that's especially complicated about it is that PECOTA is really trying to figure out two different things at once: how sustainable is this guy's batting line over the near term as he moves up levels, and how is this guy going to develop over the longer term?
A good batting eye almost certainly is helpful to a player's long-term development potential. On the other hand, if his walk rate is considerably more advanced than his power, he may experience some near-term turbulence in his stat lines until and unless the power catches up. This is a pretty common theme when looking at PECOTAs: the system may think that a prospect had a lucky year (in fact, more "top prospects" than you'd think are thought of as such because they had "lucky" years) but it may also like his skill set quite well after you strip out the luck.
The other thing about power versus walk rate is that power tends to have more room to grow. A guy with pretty good power is frequently a good bet to develop very good power; it's the one offensive skill that really continues to develop throughout a player's early-to-mid 20s. Walk rates also tend to improve throughout a player's 20s, but in a much more modest way.
In terms of Francoeur versus Hermida, I guess I'm just inclined to go with PECOTA's overall conclusion that Francoeur's package is a little bit better. If Hermida had, say, 15% more power of his own, or he struck out less, the result might be different.
Top 50 - Third Base wrote:RJ: Garrett Atkins gets surprisingly little press given that he hit .366/.434/.578 in Colorado Springs last year and might break camp with the third-base job in Colorado. The dude can hit anywhere, and I'm not sure he shouldn't rank pretty highly given where he'll play home games. Ordinarily, I don't consider a player's home venue when putting the list together; good players are good players wherever. But the Coors Effect can destroy a young pitcher, and conversely, it might give a young hitter the confidence (and job security) to ease his transition to the major leagues.
CK: Atkins won't really last at third base; he's not good at it.
NS: He's 25 and not a very good athlete, which limits his upside:
WARP: 1.8, 1.8, 1.8, 1.9, 1.6
Comps: Ed Sprague, Ted Cox, Kevin Orie
Atkins has a good chance to be a major league regular for a few years, but you have to go all the way down to Tony Perez at #19 before you find a real star on his comparables list.
Derek Zumsteg: I disagree that having a position waiting makes up for age and particularly defensive concerns, and would push him lower if we believe he's a defensive liability.
Chaim Bloom: Matt Holliday hit .290/.349/.488, and you'd think he walked on water the way they talk about him.
RJ: I guess my point is not so much that he's got a job waiting for him, but that the job involves playing 81 games in Coors Field, which will likely help him to put up numbers that are superficially impressive enough to guarantee him job security even if it's not truly warranted.
On the other hand, PECOTA's projection for next year is surprisingly cruel. It forecasts a significant drop in his true batting performance, such that even factoring in Coors, he would only hit .287/.354/.461. That's not going to impress anyone in Colorado, so maybe HM is best for him after all.
DZ: I guess that makes me even more leery of ranking him highly. If it's a guy who'll be modest in a park that makes him overrated, that modest performance, however highly regarded and whatever job security it imparts, should be what we rate him on.
Top 50 - Second Base wrote:RJ: Rickie Weeks (Brewers) is still a good prospect, in my opinion. You have to remember this was his first full pro season, and he spent it in Double-A. His secondary skills look a lot better when you factor in the 28 hit-by-pitches. A lot of players struggle a little in their first full season, especially when it comes in the high minors.
WC: I'm not sure what was going on in Huntsville, but people in Milwaukee are discounting Weeks' performance there slightly. Everyone seems to have slightly underperformed. Fielder's problems are known, yet he had the best season (still, under expectations). I think PECOTA comps on Weeks will be very telling.
NS: His numbers were disappointing but they translate to a .249 EqA, which is not horrible for 21-year-old second-base prospect with a reasonably well-balanced skill set. The main concern, I think, is his defense, as Clay gave him a -14 rating at second base. There's a good chance that he follows a Darnell Coles career path, hitting just enough to make his defense a headache.
WARP: 2.7, 2.1, 2.6, 3.5, 3.5
Comps: Clete Boyer, Chris Gomez, Jeff Blauser
RJ: On the other hand, Weeks' numbers weren't that much better than those of Josh Barfield--who had a disappointing season of his own--and Barfield is actually three months younger.
Your wisemen don't know how it feels to be thick as a brick...