Well your most compatible setup will be to use html for the whole gallery, probably generated from server code. Lightbox type tools are a slick interface feature, but yes you can run into more trouble with compatibility, people turning off JS, etc. The lightbox tools I've used fall back well when someone turns off JS, but of course the user interface is different as a result. Most Lightbox tools are set up and managed (manually) quite easily, by putting in image links that look like:
And will display both the image and a title underneath. But to manage changes, you'd be editing code like that, unless you had some sort of gallery tool (Coppermine, as an example) that would allow you to manage the whole gallery via admin tools, rather than coding it.
<a href="art.jpg" title="Mona Lisa" rel="lightbox">
Why would you want a separate browser window? Usually separate windows are the responsibility of the end user, and are not something web sites are supposed to create.
I hope I'm not making this worse...