Cassie brings up some good points in the comments on the previous post, and there's some side issues I'd like to address out in a main post.
Analogies to past actions have been wrong on several points.
About the German Saboteurs and how we should treat the Gitmo Detainees the same. First major difference, they were actors for a state power that we had declared open war on. Their attacks were sabotage, not terrorism (it's a subtle difference because most people don't understand and frankly, the Bush Administration barely understood the difference themselves). Sabotage is meant to disable response and sew chaos behind enemy lines. Their target were infrastructure orientated. Terrorism is designed to foment revolution and specifically attacks people to cause as much death as possible. And the FBI had rolled up most of the Duquesne Spy Ring before the war and used criminal trials to send them into jail for life. They were spies with military attachments. As such, they were not terrorists. While they did advocate the overthrow of the US, that overthrow would have been conventional forces taking the country, not getting the populace to fight the revolt for them. Their mission was to hamper our ability to fight Germany giving the Germans time to subdue England and solidify their control of Europe. The same reasoning behind Pearl Harbor, to hamper our ability to respond and thwart the plans of the Japanese (fortunately our carriers weren't in the harbor at the time).
About the Barbary Pirates and how this is a war. Again, the Barbary Pirates were state actors (the Barbary States). They had a solid base of operations. Also, their crimes were theft and appropriation (impressment of sailors, and theft of cargo, and destruction of ships). The Barbary States may have been "illegal states" operating within the recognized borders of other states, but they had self-governance and freedom of operation within their territories. For all purposes, they were governments unto themselves. The war was won conventionally.
So both analogies miss the mark. Al Qaeda are not saboteurs (although their attacks maybe directed this way). They also aren't state actors (although the Bush Administration declaring war on them and using the military they way they have gives them the appearances of being such). They are well funded (at a quasi-state level), but hold no territory themselves. They have no actual governance experience (as show in Iraq when they did hold territories).
Al Qaeda made the mistake of tying themselves to the Taliban (note here, the Taliban weren't their first or only hosts). We had an opportunity after 9-11 while they were still tied down. That opportunity was squandered by our invasion of Iraq (which allowed Al Qaeda time and space to re-diffuse and expand). Finishing the war in Afghanistan is now about denying them a base (and depleting their ranks and handing them a defeat), instead of rolling them up.
Terrorists are not state actors (although they can be proxy state actors as in the case of Hamas, or the real privateers/pirates who carried Letters of Marq). Terrorists are defuse (they have no defined base of operations). They act as individuals or coordinated teams. Their purpose is not to gain and hold territory, but to convince the population they should revolt. Treating terrorists as if they were state actors works to the terrorists plans. It gives them 1) legitimacy, 2) perceived strength, 3) motivation and continued recruitment opportunities and 4) sets the stage to put the populace in play. Treating them as common criminals defuses all four of these points.
The differences may seem subtle (after all, saboteurs blow up oil refineries and people die, terrorists blow up the World Trade Center and people die), but they are very important. The goals are distinctly diverse. And the after effects aren't the same.
This isn't a conflict (war if you want) about who they are, what their ideals are. This is about who we are, what we stand for. This isn't a fight they can win, it is a fight we can lose. This is what makes this conflict different.