Hughes, Bailey, and Pelfrey are all at the top. It's hard to distinguish between the three, but I'd personally go Bailey, Pelfrey, Hughes.
The next "level" would probably consist of Matt Garza, Nick Adenhart, and Andrew Miller. You could argue for both Gio Gonzalez and Adam Miller here, but I'm not too high on them. I also like Andrew Miller a lot, though he could be dropped or bumped up depending on how he develops his third pitch and how his control is in the pros.
From here, not sure. I think Hochevar and Lincecum have the most potential of the rest, but again, not sure how they'll do in the pros. Elbert is the worst of the listed because of his inability to throw three pitches. Wade Davis is a question mark but was great in A-, Gorzellany gets a start tomorrow, though I'm not a big fan. He's a Duke/Sowers-type, a crafty lefty with stuff that won't overpower anyone.
Hope this helps.
I also feel that guys like Yovani Gallardo (MIL, AA) and Ubaldo Jimenez (COL, AAA) need to be considered when talking about top pitching prospects as they have broken out in 2006 and have been dominant, propelling themselves to the top of the class. I feel like they both fit in somewhere between the elite-of-the-elite and group #2.