There is no way to actually make IE not show the open/download prompt when clicking a linked file, as that is a security measure designed to stop sites from downloading unwanted content on your machine. Just as you can, any user could alter their settings to always open FLV files, but making them do it should not even be considered. So if you want to serve video files to your users, you'd want to use an actual video player, not just a link to the file.
Html5 video tag offer plenty of options and is supported by most modern browsers, especially if you use the WebM format for your video. Here is a nice guide on how to make your own design, as all browsers display the html player differently.
The best solution, though, would be to use a player that uses both html5 and flash, so it can support all browsers, including mobile platforms. iOS, we all know, refuses to play flash except through special browsers that download the content you are viewing to their servers and send it to you in a different form. Something like FlowPlayer or MediaElements would be perfect.
The below part is not a valid answer to the OP's question, as he wants to serve FLV video on visitors. It is, however, still usefull to people who wants to configure their own IE browser to always open FLV files by default.
Save the FLV file instead of opening it, then click "View Downloads". Right click on the file and uncheck "Always ask before opening this type of file". From now on, all FLV files should open by default.
Don't you get a "Always do this" checkbox? – Kard Nails – 2014-03-21T17:43:46.267
No. I get "Do you want to open or save <filename> (<filesize>) from <site>?" with Open Save and Cancel buttons. – demongolem – 2014-03-21T17:44:59.507
You need an FLV player that integrates with IE. – Ƭᴇcʜιᴇ007 – 2014-03-21T19:40:59.587
Are your serving the flv files from a web server via some web app or are you opening these locally? i.e., is this a link on a web page, if so please tell us more about your server (apache, IIS, etc.) – Eric G – 2014-03-21T20:44:28.747
Apache 2.2 I am just testing on localhost right now. I was first seeing what HTML 5 video tags would give me then I moved on to just clicking on links to see how the videos would be presented. – demongolem – 2014-03-21T22:29:35.753
That's not the way to present video to visitors. Just serving them a link and letting their browser open it however it wants is no good. Ideally you'd want to use a Flash+Html5 player that can support all platforms and browsers. Something I recommend is MediaElements.
– Kard Nails – 2014-03-22T05:32:45.310@Kard Nails Ok I'll take a look at that and let you know if that was more what I was after. I should tell you I have tried video.js and that only allowed me to play 2 of my 6 formats. My end goal really is to avoid having to do a desktop application (which I already have for the same video formats). – demongolem – 2014-03-22T12:38:42.537
I expanded my answer below, and if you need more info, just ask. But you should know that you can never avoid everything if you want your site to be user-friendly. You will either have to inconvenience yourself, or your visitors. 6 video formats is about 5 too many. Are you sure you cannot reduce them to one common format? Or is it converting you want to avoid? The problem with so many different formats is that you have no way of knowing whether your visitors will be able to open them. Uploading to Youtube might be another alternative. What are the containers and encoding you use? – Kard Nails – 2014-03-22T16:02:54.703