Gorgeous house!! I'm sure you've looked all through houzz for photos but here are some in case you they didn't come up in your search:

http://houzz.com/photos/1003448
http://houzz.com/photos/47671
http://houzz.com/photos/1943370
http://houzz.com/photos/2082753
http://houzz.com/photos/47662
http://houzz.com/photos/40872

I'd apply finish before the stone goes up.

What type of wood is the on the house? Do you have windows that are paintable on the outside?

I would go with a natural stain or something very light. Sikkens Cetol log and siding is great. Dark green for the trim.

Good luck:)

It's great when the stone can demand attention, with the stain being more subtle. Be sure to select your stain in outside light (not indoor florescent light).

I highly recommend you do a sample test, as different woods accept the stain diffeently!! Some woods turn very orange! Unlike paint, once you stain, you can't really change it.

As for the trim, a contrast color means the doors etc would demand more attention.

Houzz is helpful - type "exterior stain color with stone" and you'll get lots of ideas!

Thanks for all the great advice and pictures!! Yes, this is cedar wood and the windows are also wood and paintable. I like the idea of going with a light or transparent stain on the siding.