In reply to Justin Tadlock.

I would prefer the option per-plugin myself. I do have a couple of very useful plugins that don't play well with others and would rather be present to update them. They usually have specific things I must do to make sure that some settings don't get over-written.

The other regular plugins I use when building have been in WP for a long time and are generally "stable" for blind updating. So having all plugins update except the 2 that I choose would be optimal. Security over convenience, I always say.