This one is pretty straightforward: Just change a pop-up's colors to background to keep it invisible, and then change to visible colors to make it pop up. But you might want to be careful about Google, since rumor has it that Google isn't crazy about making things invisible by whitening, any more than they like hidden links whose text is background color.
You may use this technique to present pop-up ads, or to solicit subscribers to your ezine, newsletter, or RSS feed. Use if for reminders, warnings, or statistics displaying. You may get survey participants, ask for donations, or use it for political fund raising. You can even inform visitors about some of your other related websites. There is no end to the types of purposes that pop-ups can be used for.
If your pop-up is about thumbnail enlargement, check out What is the easiest way to do thumbnail image enlargement windows?
If you want thumbnail enlargement without clicking, check out Making an Image Enlarge When The Mouse Cursor Is Hovering Over It