Upgrade WordPress version general question.

Hello,

I am currently running 3.0.5 and am looking to update to a new version of WordPress.

I am using Multi-DB

My question has to do with the regular disable all the plugins instructions.
For plugins that are activated on individual sub sites would I delete the plugin ?
It seems like that would not be ideal as thousands of sites would now have to relogin and activate all their plugins. How do you guys handle that? Am I missing something?

Should the plugins all be updated before before the attempt to update WordPress?
Is their a awesome document about upgrading somewhere on this site?

My plan is to setup a couple test runs on a LAMP virtual machine that I can just snapshot and revert changes.