I probably will not end up converting to InnoDB into all one file, but thanks for the information on it.
In some ways that could actually make things worse for me in the future. As it stands, since they're all seperate files repairs can even be issued individually, and even on the fly. Some repairs are much faster than others, so say a forum 5gb in size doesn't have to suffer with as much downtime as one that's maybe only 300MB. Bummer about the disk space aspect too. Also, this makes me sad:
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Backup scripts may need checking. A MyISAM table can be backed up by copying three files. There is no corresponding technique with InnoDB. Similarly, capturing a table or database for copying from production to a development environment is not possible. Change to mysqldump.
I've been doing that right now to even test what we've been going over.
We'll just see how this upgrade goes...
I have considered splitting it into a thousand databases or more before but I have absolutely no idea what that might do in regard to performance. Also the way I look at it, even if I split it up into all the databases, I pretty much have the same exact problem anyway. It's going to take time to SHOW TABLES on all of them and then run upgrades. In theory I guess each one could have rolling upgrades to a degree but I don't think it's worth it.