What software can I use to combine multiple transparent png and icon files into one transparent iconset?
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You can use a CSS Sprite generator. There are a few of them out there. You usally just upload all the icons and let the website do the rest.
I make mine by hand. I like having lots of clearly labeled layers so I can find things in the future and maintain the images. Personal preference I suppose.
You should easily be able to do that by hand in Photoshop. If you'd like to automate it, I'd see if a Adobe Bridge's Contact Sheet feature gets you what you're after.
Information and video: Creating Contact Sheets in Adobe Bridge
if you are looking for windows ico format , you can use this plugin for Photoshop . but it's bit old though.