I think that certain constraints need to be placed upon them. For example, I think that any 501(c)(4) "social welfare" organization that donates to a Super PAC should be required to make its donor lists public record. This eliminates the ability to engage in political money laundering by going through a 501(c)(4) and then a Super PAC and thereby enjoying both unlimited contributions and anonymity.
Beyond that, though, I am hesitant to try to make Super PACs illegal. The name "Super PAC" itself is not even a legal thing: it was invented to describe something that people do to take advantage of laws as they are. Attempts to "take the money out of politics" in the past, such as McCain-Feingold, have actually backfired to some extent in that all they do is raise the bar a bit rather than fundamentally changing the way things are done. A raised bar can just mean that an even more unfair advantage is given to those who figure out a way to legally cheat. For example, in limiting the amount each individual can give to a campaign committee, campaign finance laws just brought about the rise of "bundlers" - people who specialize in brining lots of folks together to donate. When this happens, while politicians are not so beholden to a small group of deep-pocketed donors, they do become beholden to bundlers. We can expect that, even if we ban Super PACs, people will just find another way of using their cash to influence politics.