You can use any one of the widely available drawing libraries.
jsDraw2D[
^] has some samples at that link and it's fairly easy to use.
If you need to support transparency, I think you need to venture into canvas. Check out
gamejs[
^] docs and samples here.
EDIT: My apologies...I thought that you were meaning to let the users DRAW polygons on first read. You can still use method #2 above and incorporate CSS to do the highlighting (on hover, for example).
The other approach would be to use PhotoShop (or a similar tool) that can do 'slices' with hover-over scripts. These usually work in all browsers and are relatively easy to do if you've got the source images. You'll create a 'highlight' layer that is revealed with a mouse over. Lots of tutorials out there so Google away!
Cheers.