The general stance on using plug-ins is split between "go for it" and "don't ever". I think more of a balance is needed. Any reasonably sized website will usually end up using some kind of plug-ins at some point. What you use, and how to use it is the key. Your decision to use any plug-in should be strongly based on whether it's reasonable to believe that most of your audience would have the plug-in already installed. Since it's impossible that all of your visitors will have it, you should also keep in mind how much of a hassle it is to install it.
Here's my take:
Java applets
This is one of the only places I take the stance of "never ever"; almost. Unless you're in the rare case that you need functionality that only an applet can provide, don't use it. The plug-in is very processor intensive to load (my mouse stops moving when it starts up) and once it's in memory there's no way to get it out of memory aside from closing your browser.
The grossest misuse of applets I have seen is one site that had four applets for four navigation buttons. The only effect the applets provided was changing the background color on the button when the mouse moved over them: an effect that can be achieved with three lines of CSS. For the sake of all that is holy and good, please don't do this.
If your users don't have the Java runtimes, it's a 15MB download. This is a piece of cake for broadband users, but those still on dial-up will be waiting close to an hour or more for this baby.
ActiveX
Here is another thing to stay away from. This is because unless someone is using Internet Explorer on Windows, they'll probably be out of luck, or have a lot of trouble. While most of your audience will be able to access the ActiveX features without a problem, it is bad policy and business to limit your audience at all.
Flash
This can replace much of the functionality people want when using Java applets, and more. It is great for adding that extra kick to a site. Be careful not to use it too much though. While making an entire website in Flash is cool, search engines can't pick up any text in flash pages (yet). Also, many web-savvy users despise Flash-riddled sites, so know your audience.
Flash objects take no extra time to load apart from downloading the Flash file itself. If you're making an animation, or anything that needs to be fully loaded before watched or used, include a loading bar so the user isn't sitting there wondering what's going on.
If your user doesn't have the Flash plug-in, it's an incredibly small 684K download. That's only 2 minutes for a dial-up user.
Streaming audio/video
Do a lot of research here. Don't go off only what I say. There are three main-stream options: Windows Media, RealPlayer, and QuickTime. If most of your visitors are Windows users, then Windows Media is a safe bet since it's probably already installed. If you think there will be Linux or Mac users in your audience, I would suggest QuickTime. RealPlayer is generally disliked and is less popular. But again, do your research as to quality, speed, and cost before you decide.
You may even consider using Flash for audio or video (YouTube does this) since more people have Flash installed. You can make your own play/pause/stop control to look however you want.
Sometimes the best option is to let the user download the entire file in a standard format (.mp3 or .avi suggested). This way, they can play it themselves in their media player of choice.
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