Did Mail.app once allow messages to be annotated with notes? I thought I remembered being able to add notes to a message in a pane over the main message (as well as todos). In Lion, I don't see how to do that. I can create individual notes but not annotate a message. 

Am I remembering correctly? Is there some way to get that feature back in Lion (without using MailTags, which won't sync across machines with my Gmail accounts)? 

I never really cared about the feature but found a use for it just this week.
yes and no
yes: it was possible to "annotate" mails with a todo - that function is gone in Lion

no: afaik it was not possible to "annotate" mails with a note as well