The most common cases where these can be used are :
(1) When you want to draw attention to important information.
(2) When you want some action from user to continue
(3) Showing warning signs
(4) For extra options panel (like login/register panel)
(1) Prototype Window
(2) Simple Modal
Simple Modal is jQuery framework based plugin which can be used to create different types of modal dialog boxes. This plugin is cross browser compatible.
Modalbox is based on Prototype and script.aculo.us frameworks.Modalbox is lightweight (10kb) and produces valid XHTML/CSS code.It uses ajax instead of iframe to load content and is also cross browser compatible( Tested in IE6, IE7, Firefox 1.0, 1.5, 2.0, Safari, Camino, Opera 8 and 9).
Moodalbox can be used to display remote content using Ajax. It is based on mootools framework.
It is plugin for jquery framework to make modal windows and dialog boxes in a web browser. features include multiple modal (including modal in modal) support. jqModal is lightweight(2.9kb), powerful and flexible.
(6) Livepipe UI
Livepipe Ui is a suite of powerful widgets and controls for websites. It is built on prototype javscript framework. Well documentation and highly tested controls are just some of it’s features.
It is jquery based, facebook style lightbox which can be used to display images,divs or entire pages.
A way to make dragable modal boxes.
(13) Suckerfish Hover Lightbox Redux
A suckerfish dropdown menu containing images effect. A really nice and unique effect.
(14) Interface Elements for jQuery
(15) Sexy alert box
(16) jQuery Alert Dialogs
(17) jQuery Block UI
The jQuery Block UI Plugin lets you simulate synchronous behavior when using AJAX, without locking the browser. When activated, it will prevent user activity with the page (or part of the page) until it is deactivated.
(18) jQuery Impromtu
jQuery Impromptu is an extention to help provide a more pleasant way to spontaneously prompt a user for input. More or less this is a great replacement for an alert, prompt, and confirm.
nyroModal is a highly customizable modal window plugin for jQuery.
jGrowl is a jQuery plugin that raises unobtrusive messages within the browser, similar to the way that OS X’s Growl Framework works.
(22) Lightbox gone wild
(23) Lightbox 2
This is good old lightbox that most of us probably already know about.