Plagues

[Kekvit Irae]

Quaratine usually isnt the best solution, especially if you have tough-as-nails agents that just wont die from the plague.
Usually it is the infected agent or family member who is keeping the plague from dispersing in your city. Move all of them out, seperating the healthy agents and family from the infected, to an open tract of land nearby, and let them either die or heal up.
More often than not, the city plague dies out a turn after I do this, and all I need to do then is wait for the plague to die out on my characters before moving the infected people back in.

[MajorFreak]

i agree with Kekvit, don't quarantine immediately - remove each agent/general to it's individual spot around the city - then quarantine. With patch 1.2 they tend to get over it quicker (and die faster)