Try disabling hardware acceleration in Quicktime, and updating your video drivers.

Also make sure your plug-ins are up to date. See:

https://www.mozilla.org/en-US/plugincheck/

Also see the help article:
Use the QuickTime plugin to play audio and video

I'm up to date with quicktime. Will "disabling hardware selection in my quicktime have any effect on what my clients see who have updated to 8.0.1. That is the problem. Or do i need to start exporting my movies out as html5?

Disabling your hardware acceleration only affects your own machine, and changes how your video driver actions are treated by Firefox.

If the problem is a choppy appearance on your own machine, disabling hardware acceleration means that you stop your own machine from trying to outperform the Quicktime software.

If the problem is that your clients see a choppy video, then the problem could be with the video itself or with the clients' own hardware acceleration settings.

You could provide a sentence of instruction with your videos to your clients (like a note on the video page), telling them to change their video acceleration setting if the video appears choppy to them.

Your Quicktime help manual should have a section on hardware acceleration and how to work with it.

Most browsers, including Firefox, make use of contemporary hardware acceleration abilities, and this can have effects on how video is rendered, but the issue is less one of how a browser functions, than how the video rendering software is working.

HTML5 is a forward step toward cross-browser compatibility, and is very nice because users don't need to install any third-party software, therefore it is much more user friendly, and my own opinion is that when it can be used, it should be used rather than forcing third party products on clients.

The problem with HTML5 video is that the "standard" isn't official yet. The "format" is up in the air.
http://en.wikipedia.org/wiki/HTML5_video#Table

Apple (Safari) and Microsoft (Internet Explorer) are pushing the closed source H.264 (those two companies are partners in the group that owns H.264) which is free for users (for now) but will be costly for vendors and commercial users of H.264. Whereas Mozilla, Google, and Opera are backing an open source format, that is royalty free for all. OGG /Theora or WebM.
http://en.wikipedia.org/wiki/WebM_Project

Whichever format is eventually selected for HTML5 video, some users are going to have to install something. With Google Chrome and Mozilla Firefox being like 60% of the browser market, the sensible choice for a standard format would be WebM - plugins are available for IE and Safari, the rest support WebM. Apparently there is no OGG/Theora plugin available for IE, and without a plugin it is a non-starter.

So I'm basically just a simple photographer. But from what I understand my Quicktime tours will no longer run smoothly as they have on all browsers for the last four years with these new updates? Unless I change to a new file format which is yet to be decided? The tours run fine as individual quicktime files so it is not quicktime. They just start to operate badly once loaded into the web template/skin and viewed on these updated browsers. Take a look at an example on the new firefox browser and than check it out on an older version or safari all is good.

http://spinvirtualtours.com/tours/new_vtour/1045_skyland_dr

If you check the drop down in the lower right corner of the tour template and choose "save as quicktime movie" and then just click the movie it runs smoothly from the desktop.

It is already a big enough job to get people to be able to view these so the idea of having to give people more instructions to go in and change setting is Quicktime isn't realistic and I couldn't even figure it out. (Not surprising because I am not a programmer.) One of my competitors uses Flash which I thought would die out while Quicktime and Html5 would become the norm. At least the flash tours are reliable on these updated browsers. I'm confused and frustrated since delivering these tours is half the revenue of a very good business and all of a sudden they work terribly.

Looks a little choppy to me in Firefox 3.6.24, too - not just Firefox 8.0 - using Quick Time Alternative Lite 4.0.1 which uses the Quick Time 7.6.9 plugin in Firefox. (I won't install Apple's legitimate Quick Time program and then spend an hour fixing all the file associations it breaks. Thanks Apple, once was enough for me.) There also seems to be a zoom-out just after the start of that video after the windows on the left are half gone, which makes me a bit dizzy as it slowly zooms.

My advice is to "bet" that WebM becomes the HTML5 video standard, and even it doesn't become the standard format all current browsers support it or have manual installation plugins available for WebM (IE and Safari), per that Wikipedia article.