Two Options
In the beginnings of the internet there was only two options for animation on a webpage. The first was animated gifs, an animated gif is essentially a web-based stack a flip cards, stringing together static images to create the illusion of movement. Unfortunately animated gifs can end up being large files, pixilated and don't look very sharp. In 1996, Macromedia released a product named Macromedia Flash. This was a vector based animation platform that allowed web designers to create animations using tools provided by Macromedia.
This resulted in smaller files with cleaner animations. The major drawback to this was it required a browser plugin to view and most of the internet wasn't on board with this yet. Now days, there are better options then animated gifs when it comes to adding features to your site. With the new advances in HTML and JavaScript, major browsers vendors are investing huge efforts in improving JavaScript engines in their browsers. With all of this new attention to JavaScript dozens of frameworks, have popped up as tools for web developers to use. Common frameworks include jQuery and jQuery UI, YUI, Prototype and Scriptaculous, and the Dojo toolkit. When it comes to deciding between JavaScript based features and Flash based features in your site there are many different advantages and disadvantages you need to weigh.
JavaScript
JavaScript has several distinct advantages over Flash, first it no plugin is needed because it uses open Web technologies like Document Object Model, HTML and CSS. Secondly, it is much easier to make animations that are accessible and 508 compliant and JavaScript is also viewable on many mobile devices, unlike Flash applications. Although, jQuery/ JavaScript cannot be used for all animations, when it comes to certain types there are things that jQuery just can't do. It cannot handle 3D animation, audio/video players or fine user controlled animation. When using JQuery you are also at the mercy of user end controls such as disabling JavaScript in a browser and resized text. Is it in the budget?
jQuery or Flash
When considering whether to use a jQuery or Flash based solution you are also going to want to look at the development and maintenance hours versus what the features are that you are looking for in your project. JQuery can be used for almost all modules for a standard website, including scrolling images for the banner and photo galleries, interactive menus, form validation, and pop-ups and tool tips. Because most of these tools are available as JavaScript frameworks this can end up keeping the development costs of your site down. All of these features can be integrated with the CMS and dynamically updateable.
Changes to the design of jQuery features most front end designers can handle and this will lower any maintenance costs you may incur. A Flash application encapsulates all the code in the application itself. First, this means creating the application require the use a specialized Flash developer, but this can be to your advantage if you are looking for features to your site such as audio/video player or 3D animation. If you are looking to have complex multi-media in your project, you are going to have a higher development cost. Changes and updates to Flash content can be executed via updateable XML files, but if you want to change the design of the application you will need to use a Flash developer with can cost more in maintenance hours. What this decision really comes down to is asking yourself what are the features that you need. Much of the "flash" in Flash can be mimicked at a lower cost with jQuery, but if your site is multi-media heavy; your best option would be to go with the Flash application for the ease of the end user and yourself.