Version 4 of Painter has built-in tools to help create graphics
for the web. Transparency is designated by using a mask and a
threshold setting. See chapter 7 of the Tutorial manual for more
details.
Ok, so Illustrator technically isn't imaging software, but it's
new rasterize option and GIF89a plug-in put it on this list. I have
no idea if this is different from the Photoshop version, but
you can find out for yourself. The Illustrator product info
page (above) steers you to downloading
instructions.
I admit it: this is a short list, but I only know about the products I've
used. If you want to see product info added to this list, click on the
Comments link below.