Capturing a were creature and using it to create an army of regenerating super soldiers. I've got plan for the quarantine barracks all laid out and everything, but every werecreature I encounter either dies instantly to hunters/caravan guards or runs away before it gets to my werecreature trap.
Plans? Can I see them? See, the problem is the reverse for me, I have a were creature but no safe way to infect a soldier without the creature dying 
Sure! Keep in mind that this is all very much untested, since I haven't been able to capture one for my own needs yet.
Werecreatures can be assigned to chains, so the 'initiation room' is just a 3x3 cell with our werecreature "Patient Zero" chained in the middle of the room. A single door leads to a narrow hallway filled with cage traps and capped by a raising bridge, just in case something goes horribly wrong and we need to seal the room and recapture Patient Zero.
To infect our military dwarf "Initiate", we put him in a one-man squad. He is fully armored except for his hands (to help ensure he receives some non-lethal injuries) and carries no weapon. To minimize risk to Patient Zero, Initiates should be novice recruits - they'll have plenty of time to train and spar when they're locked away from society in the quarantine (more on that later). When Patient Zero turns into its werecreature form, we order the Initiate into the room and lock the door. As soon as our initiate has been bitten, we cancel his military orders and unlock the door. The dwarf is then assigned to a burrow in the quarantine barracks. Note that your medical dwarves will probably try to patch up your initiate - this is okay, just make sure they have no other jobs assigned and a plentiful supply of medical equipment. Failing that, make sure you can seal off your hospital. It might be wise to set up your hospital zone with individual patient rooms, each of which can be sealed - especially if you have multiple Initiates at once.
The quarantine barracks is basically a mini-fort. It should have sleeping quarters, a dining room, some happiness-generators, etc. You can either make it self sufficient or drop supplies in through holes in the ceiling. The Initiates enter through an airlock, using either artifact doors and forbidding or bridges to ensure that there is no way in or out under normal circumstances.
The key problem with a quarantine barracks is that werecreatures gain the 'building destroyer' tag when they turn. It's not really practical to have to rebuild all your quarantine's furniture every month. To circumvent this, a long corridor is attached to the quarantine leading to a set of pastured bait animals. Building destroyers favor creature destruction over building destruction, so each month your initiates will turn and charge down the corridor rather than breaking all the beds and tables. Once they are in the corridor, pull a lever to trap them inside with raising bridges. You might even be able to work out some crazy automation scheme with pressure plates and such, but I don't have any experience in that. Artifact doors would probably make this easier, if you're lucky enough to have several of them.
A third bridge the the corridor is normally closed and opens to the outside. When a siege hits, bottle up until the full moon, then open the gates and let your rampaging lunatics outside. Alternatively, make the bait animals do double-duty and use them to lure invaders
inside, where the invaders are forced to do battle with your werecreature army in close quarters. A final possibility is to let your dwarves outside
before they turn and have them deal with the army the old-fashioned way, relying on regeneration to cure them of any injuries they suffer - this is probably the best option if your Patient Zero is a weak little werehamster or something.
Again, I haven't been able to put this plan to the test yet, so implement this at your own risk!
A final thought - if you're having too much trouble keeping Patient Zero alive, it might be worth it to try dropping your Initiates into the room from above using a retracting bridge one z-level up. If the initiates are currently set as civilians, they should run away from Patient Zero instead of attacking.
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