I have a bunch of test footage, behind the scenes, etc that I want to put on a bonus DVD. Should I still export each individual video uncompressed and let Encore handle transcoding them all once they are all in the project? What method do you think gives the best overall quality for all the clips?

I also have WMV versions of alot of the videos. Should I use those to preserve space?

A "Bonus" DVD is just another DVD. I've done a few of them exactly the same way as regular feature DVDs and BDs.

What can differ with bonus disks is how you structure the material. A feature is linear. Bonus disks don't necessarily have to be, so you have some organizational options. I don't think there are any preset rules. Do what makes sense for you.

.wmv files won't play in DVD players so they'd have to be transcoded. Substantial quality loss doing it that way. Stick with the highest quality master you have.

So should I export all of the clips highest quality and let Encore transcode them down? How many hours can fit before visible quality loss would occur?

Yes, export at highest quality and let Encore decide. If you have less than 2 hours of footage total (including the main title), then the final quality of the footage will be high. Any more than 2 hours and you will start to see some artifacts creeping in.

If this bonus footage is on a stand along DVD then 2 hours of footage will be OK.

ok now I just need to find the space to hold all the uncompressed video lol