Navigation
This is the most common way of abuse, Flash navigation is extremely bad for a number of reasons:

-Search Engine Optimization: having text on your website is the most important thing. Search Engines use text for indexing your site. The problem with Flash is that the search engines do not go inside Flash files to collect the text information.

-Page loading time: Using Flash for your navigation will slow down the loading time for your web page.

-Not user-friendly: Two things, the aim of website design is to provide simple navigation throughout your website. In Flash navigation the visitor must wait for an animation to load completely each time their mouse click an item. People hate waiting!. And the last thing is that not everyone is using Flash.

Flash Intros
The worst way to use Flash is on your website’s intro. Most people are impatient when surfing the web, many of them do not have patience to watch a Flash intro.
If it is impossible not to have a flash intro, please, include a “Skip Intro” button that is clearly visible to the user. But we think that there is to try to avoid the flash intros.

OK, But, What is the Best Practices in Web Design?
The best way to build a professional website is by using CSS (cascading style sheets). If you need more information, visit http://www.w3.org/Style/CSS