I am listing this as an enhancement as I think the official clients do this too.
When I log on, Adium receives the messages that were sent while I was offline. If I am in a state with an auto-reply, it sends that in response to the old message, effectively announcing that I am online, even if it is an away or invisible status. For the accounts that log on automatically when I start Adium, there is no time to prevent this.
At the moment, I just switch to a "quiet" state before I log off, but that's a bit of a pain with eight accounts. It would be worse with more, I assume.
I would like Adium not to automatically respond to messages that were sent before I logged on. One slightly cheesy but highly effective way to do it could simply be to have it not auto-respond to messages received within a few seconds of logging on. Not sure if that's any easier, though.