What color is the background? If you have mainly one color of fabric behind the applique, go with that ... otherwise, I agree with busy fingers that grey is your best bet.
You also want to be sure to use a 50wt cotton thread for the quilting (or higher) because it will meld into the fabric more and you notice mistakes much less. You also may want to consider whether you want to quilt over the applique at all. Depending on the size of each applique design, you may be able to just quilt around the design, which would probably help limit your choices even further. Among the remaining choices, I'd usually pick the least saturated color.
But no one's to say that you have to only use one color for quilting the entire top. I think it's fun to machine quilt around my applique with one color, machine quilt my border in another color with a different pattern & then do some small scale quilting by hand inside the applique, matching my thread to the color of the applique. I'm sure it will be beautiful no matter what you do.
