Why lightbox is bad.
It's cool and all, but really it just annoys your average visitor.
There's a golden rule when it comes to web usability (especially in this day n' age of web2.0'ism), and that's to keep things simple. Lightbox is anything but simple. It's simple in execution, sure, you're just viewing an image, but all of the extra bells and whistles are entirely unnecessary and I'll explain why.
Unnecessary animation!
Some "lightboxers" have the scrolling animation before the image will actually load. One word: annoying. At first I was like "oh that's cool!", but after the 2nd time I realized how much of an annoyance it is to have to wait for an unnecessary animation. People want their content and they want it fast. For those that are less internet savy, they don't know about the whole "right click / open in new tab or window" option.
The rest of your website becomes useless
Since lightbox uses a div that dims out the rest of the site, the rest of the site becomes unusable unless you either click "close", hit the "x" key, or click on the background. Extra work, no matter how little it may be, can become very annoying with a bunch of lightbox based images.
Confusion
If you use lightbox on a site with a demographic of non-internet savy visitors, you're going to confuse people, I guarantee it. Another golden rule in web usability is to assume every visitor has the intelligence of a 3rd grader.
It's not unique anymore
Something once really unique has been made typical and boring. It's old, it was a decent idea for 10 seconds and now it just annoys everyone. If you want a unique site, don't use lightbox, everyone and their grandmother is using it.
Those are just a few that I've thought of off the top of my head. I'm sure there are others. A great alternative I like is using a hover preview of the thumbnail. An example of that can be found at my logo portfolio, simply hover over the thumbnails and you will see what I mean. It's fast, easy, and doesn't hijack your browser.