As far as I know, it began with showing a picture or slideshow. Darkening the rest of the screen has the effect of turning down the lights in the room. Thus, in itself, the lightbox-style is an effective means to concentrate the users attention on a popup message. However there can be a number of issues.
The first of which is that the “close” button is often tiny or hard to find. I do not want to waste my time trying to figure out how to get rid of the popup.
Some have had popups on each page. This probably goes back to cookies and security settings that don’t store or keep them between sessions. I’m in the latter group because I don’t want a zillion little cookie crumb files littering my computer. (That is subject of another Rude List item in the future.)
Another problem is if the window is too small because of a small or lower-resolution display. Think about tablet users, mobile phone users using the desktop version of your site. I have seen sites where the popup ran off the screen and it was literally IMPOSSIBLE to continue. Sorry, in that case, my business went elsewhere just because I couldn’t reach the site.
Thankfully in my Staples example here, I could click outside the popup and still proceed but it is still annoying.
First, make sure the close buttons is clear and easy to activate, even on touch screen devices. Furthermore, process clicks outside the popup and use that as an indication the user wants to close the popup.
Next, I would also make the popup close itself after a few seconds and never come back, cookie restrictions permitting.
Finally, really consider if such an intrusive popup is really necessary. Is the message THAT important? Does the message even apply to the viewer ? For example, in the case of Staples above, I already have their Rewards card, and yet I continue to see the messages. That happens a lot !