It would be interesting to compare how many people were unlawfully detained under both administrations.
Incidentallly, how many people did Hillary have arrested?
Well, obviously the Bush administration would insist that they haven't detained anyone "unlawfully" because they would insist that all their "detentions" have been justified either by the Patriot Act or by powers granted to the executive, however I suspect that if Thomas Jefferson were alive today he would vehemently disagree, so I think it's safe to say that your inference that Bush has had far more questionable lockups than Bill Clinton.
However, it also has to be admitted that the Clinton White House is reported to have repeatedly demanded FBI files on his political opponents and a discouragingly high number of his opponents were hit with IRS audits, including IIRC Paula Jones herself.
A better question might be, had 9/11 happened on his watch, how would Clinton have resonded.
For starters, since Bill Clinton tried to pass a bunch of laws following the Oklahoma City bombing that were almost identical to the Patriot Act, I have little doubt that following an event that dwarfed the OKC bombing like 9/11, had such an event taken place in his Presidency we would have seen an even more restrictive Patriot Act.
Furthermore, while I'm no fan of John Ashcroft, I think anyone familiar with Janet Reno's career would have to agree she would have been, if anything, even more reckless when it came to civil liberties issues than either Ashcroft or Gonzales.
In short, I see no reason to think the Clinton would have had any more qualms than Bush about "unlawful detentions."