1. Jared Goff, QB, California. It was a difficult choice between Goff and Paxton Lynch here, but Goff is the slightly more NFL-ready prospect of the two. Goff has generated comparisons to Matt Ryan from NFL scouts, while some other scouts question his struggles in a couple of games this year. Does throw occasional interceptions, and doesn't run as much as Lynch, but he has the better arm of the two. From a pure passer perspective, Goff is, in my opinion, the best fantasy quarterback in this draft class depending on where he is selected (which should be somewhere in the 1st round of the NFL draft). Should be an NFL starter.
2. Paxton Lynch, QB, Memphis. Lynch is another player who should be drafted in the first round of the 2016 NFL Draft. His throws are slightly less accurate than Goff, but Lynch is a better runner. He's rawer than Goff and might need some time to adjust to the NFL, but from a long-term perspective (if you're in a dynasty league, for example), Lynch deserves a long look along with Goff. Lynch is another guy who should be an NFL starter.
3. Carson Wentz, QB, North Dakota State. If Goff and Lynch are the top tier of quarterbacks in the NFL draft for fantasy, Wentz starts out the second tier. Wentz is a potential NFL starter who could be drafted early in the 2016 NFL Draft (potentially late first or early 2nd round). While he did miss much of his senior season due to injury and is from a Division I-A program, Wentz is an intelligent player who doesn't make mistakes. Not the greatest arm in the draft, but he's not a guy that will kill you with poor decision making. Similar frame to Ben Roethlisberger. I wouldn't target him yet for redraft leagues (unless we find out that he will be starting for whatever team drafts him), but he could be a good target for dynasty leagues if you have an established starter.
4. Connor Cook, QB, Michigan State. Cook is a guy who, like Wentz, could be an NFL starter. A few weeks ago, I would have swapped Cook and Wentz, but Cook's bowl game performance was pretty bad, and that might scare some NFL teams away from him as a potential starter. That being said, from a performance perspective, Cook may be the better long-term prospect. He played late in 2015 with a shoulder injury, so that may tip the scales in his favor for scouts, and Cook is already comfortable playing in an NFL-style system. The decision between Cook and Wentz is a tossup at this point; I think Cook is the better prospect of the two, but Wentz could wind up with a slightly better situation.
5. Dak Prescott, QB, Mississippi State. Prescott is a guy that intrigues me. He's been described as some scouts as Tim Tebow 2.0, but the similarities may be more due to the fact that he played under Tebow's college offensive coordinator, but Prescott may be the better NFL prospect. He's a guy that could find a starting role and keep it but also might also spend the bulk of his career as a backup. If he does wind up in a good situation, he could put up some solid fantasy points; he's a guy that generates a large number of rushing touchdowns and also has a decent arm. The upside is there for him to be good for your fantasy team, but he needs a good situation to be fantasy-relevant. More value in dynasty leagues than re-draft leagues.
6. Cardale Jones, QB, Ohio State. I have no idea how to slot Jones. He showed tons of potential as a starter with Ohio State last season, but was also benched this season. Last year, he could have been a top-15 prospect in the draft, but elected to return to Ohio State for this season. Jones has the tools to be a potentially good NFL quarterback, but he could also just as easily fall into a career backup-type of role. He's a guy to monitor heading through the draft process, and if he lands in a good situation, target (especially in dynasty leagues).
7. Christian Hackenberg, QB, Penn State. Hackenberg has struggled with inconsistency through his career at Penn State. He has the physical tools to be a good NFL quarterback, but he has failed to put up solid numbers at Penn State. He also has been extremely incosistent as a starter. That being said, he was recruited by Bill O'Brien, and could potentially be drafted by Houston as a potential starter. If that happens, then Hackenberg's fantasy value would skyrocket.
8. Jacoby Brissett, QB, NC State. Brissett is likely a guy that will likely wind up as a career backup, but some scouts have him rated higher than Hackenberg. I think he's a better passer than Hackenberg and has more upside myself, but that Bill O'Brien connection keeps Brissett rated slightly behind Hackenberg in this list.
9. Kevin Hogan, QB, Stanford. I like Hogan better as a player than Jones, Hackenberg, and Brissett, but as a fantasy player, those three might have a bit more upside. Hogan struggles with inconsistency issues; when he's on, he looks like a potential NFL starter, but in his bad games he doesn't look NFL-ready at all. Will likely be a #2 in the NFL, but if he lands in a good situation and matures as a player, the upside is there for him to be a solid player in the NFL. He's a guy to target later in dynasty drafts and watch develop.
10. Cody Kessler, QB, USC. Kessler is an intriguing prospect that could develop into an Andy Dalton type of player; the big knocks on Kessler are size and arm strength. Then again, Russell Wilson was too small to play in the NFL and Andy Dalton's arm strength was a big knock heading into the draft. While Kessler likely projects as a backup, in the right situation, he could emerge as a potential spot starter and could do well.
Stopping at 10 for now since it is difficult to get too deep into rankings without a deeper knowledge of player situations moving forward. Every season, many decent college quarterbacks never make it onto an NFL roster. This year will be no different, and most leagues will not draft more than 10 rookie quarterbacks in 2016. Trevone Boykin is an interesting player who missed my list; his legal issues could make him fall into undrafted territory in 2016, especially since he may wind up transitioning to WR at the next level. Watch his situation moving forward. He's a guy that could wind up being at least worth considering at the tail end of a dynasty rookie draft depending on where he falls. I'll get more in-depth with rookie fantasy coverage as we work through the draft prospect, but this list should at least get you a start on quarterbacks. Good luck, and happy scouting!