I thought not one table per user, but rather one table for all messages. On betawiki are a lot messages e.g. http://translatewiki.net/wiki/MediaWiki:Abusefilter-revert-title/en.
I also think a global table would be better, because it's easier to sync, and there's no need to create new tables all the time. It would also allow common messages to be recycled. On the other hand, if people are not careful about prefixing message keys, it could easily lead to conflicts.
So I propose a four field scheme: language, *application*, key, message.
The application field would remove the need of prefixes. To allow for common cmessages, we could have some special applications like "toolserver", "common" or something. We could also import mediawiki messages as an application called "mediawiki" - a lot of common stuff is covered there, in a lot of languages.
I think i could get such a database up pretty quickly, though i'm not quite sure yet how the sync could be done automatically. I'll talk to siebrand about it.
-- daniel