How can I configure my phone to automatically connect to remembered wifi networks? (after having left the device to sleep)
I have this same problem, intermittently, with my N1/froyo/CM6. I don't know why it happens, but it's been happening since the froyo update afair. 

I've noticed it happens less often if I stay in one place. This led me to the theory that, since I live at a university, the fact that networks will pop in and out of range even as I enter my dorm and walk up to my room will make my N1 think that the network's unstable and thus disable it.

Toggling definitely fixes the issue.