In my post above "but it is had to add" should have read "but it is hard to add". Darn spelchex.
Exporting using Animation codec wouldn't "degrade" the video quality but it also wouldn't allow you a method of setting the transparency color unless you had some "high end" video editor software.
This is one reason I have two machines and multiple OS's running on them.
Since Apple no longer sells a QuickTime version 6 Pro registration the multiple OS method may not work for you. I routinely work with version 6 and 7 and swap files as needed. Once the transparency level has been "set" even version 7 understands and allows it.
And the color picker method may not be the best use, anyway. It would render any chosen color (from a palette of 32 million) as transparent anywhere it was used in your file. So. A white background around a "talking head" shot would also render the white shirt worn by the "newscaster" as transparent.
Just like an image editor, QuickTime can set alpha "layers" onto a video. But, unlike an image file, video "moves" so it's difficult to add a mask or alpha channel outside a dedicated app like Final Cut Pro or other video editors.
I use "text tracks" in some of my QuickTime files and version 7 shows a "box". Since these text tracks translate as "vector" formats (scale without degrading) I only add them using QuickTime version 6 to add transparency. An example:
http://homepage.mac.com/kkirkster/LemonTrees/LemonTree.qtl