I have this selector below where it ignores any li with the class show-all-boxes
li
show-all-boxes
$(\'.boxes li:not([class=\"show-all-boxes\"])
The :not selector can take multiple CSS selectors as arguments ( http://api.jquery.com/not-selector ). E.g.
$('div:not(.a,.b)').empty()
http://jsfiddle.net/HFfcP/
try this :
$('.boxes li').not(".show-all-boxes, .show-all-circles, .show-all-triangles").find('input:checkbox')