Slightly Counterintuitive, But Works Rated 4 out of 5 stars
CheckFox 0.9.1 works for me in FF 3.6.4, but isn't the most intuitive method. You have to select a text area, encompassing the check boxes you want, and then right-click the text area and click on "check" in the context menu. It'll then check any boxes within that selected area. It's a little tough, because the text isn't always uniform or in the same field (tables or frames for instance), and the checkboxes don't highlight - making it initially hard to tell if you have the correct boxes selected. Still, despite this minor difficulty, CheckFox does help you check multiple checkboxes quickly after you figure it out.
CheckBoxMate 0.2 was far more intuitive, but has yet to be updated for use with 3.6, even if you try to override compatibility.