I share your concerns, and it is complicated. Check out http://volokh.com/ for an excellent roundup of links and reactions.

This one is especially good.

Scalia's dissenting opinion on the Rasul case is a good fisking of the court's opinion. Read it here.

Here's his concluding paragraph:

"Departure from our rule of stare decisis in statutory cases is always extraordinary; it ought to be unthinkable when the departure has a potentially harmful effect upon the Nation’s conduct of a war. The Commander in Chief and his subordinates had every reason to expect that the internment of combatants at Guantanamo Bay would not have the consequence of bringing the cumbersome ma-chinery of our domestic courts into military affairs. Con-gress is in session. If it wished to change federal judges’ habeas jurisdiction from what this Court had previously held that to be, it could have done so. And it could have done so by intelligent revision of the statute,7 instead of by today’s clumsy, countertextual reinterpretation that con-fers upon wartime prisoners greater habeas rights than domestic detainees. The latter must challenge their pres-ent physical confinement in the district of their confine-ment, see Rumsfeld v. Padilla, ante, whereas under to-day’s strange holding Guantanamo Bay detainees can petition in any of the 94 federal judicial districts. The fact that extraterritorially located detainees lack the district of detention that the statute requires has been converted from a factor that precludes their ability to bring a peti-tion at all into a factor that frees them to petition wher-ever they wish—and, as a result, to forum shop. For this Court to create such a monstrous scheme in time of war, and in frustration of our military commanders’ reliance upon clearly stated prior law, is judicial adventurism of the worst sort. I dissent."

This time, Scalia has a point. Hmmm....

I mean: ...unlike a year ago.

Scalia's complaint strikes me as a bit silly. (Scalia generally strikes me as a bit silly.) So he's concerned about forum shopping since under the court's ruling the detainees could theoretically bring their habeas petitions in any of the 94 district courts. It strikes me that that could be easily rectified: congress could pass a statute assigning jurisdiction to one district court, or establish a special court to hear such cases. Moreover, it isn't clear that a statute would be necessary: it has been a while since I looked at it, but, if memory serves, there is a "multi-district litigation" procedure by which the administrative judges of the various district courts can effectively consolidate cases involving similar legal issues in one district. It strikes me as a bit silly for Scalia to moan about procedural issues when important constitutional protections are at issue.

BTW, "innocent until proven guilty" is a statement of procedure in court. On the other hand, given the credibility deficit of the current administration, I would hate to be considered guilty of something merely on the say-so of the likes of Bush, Rumsfeld or Ashcroft.

Innocent until proven guilty. Sounds good to me!