The only thing I am stuck on optimizing is InnoDB tables for the MySQL server. If someone has experience with that table type, please let me know. I made some settings, they seem to be fine, but I would prefer hearing from someone with experience.
Sorry, all my MySQL experience is with MyISAM tables. But, if you have any specific questions that may not be table specific, let me know. I probably won't have much to offer, but you never know.
To me, the two big generic db optimization tricks are:
(1) Don't use varchars where you can use integers, especially on columns that are used in the where part of "select...where" statements; think about how much faster a computer can compare integer numbers than search for strings/regular expressions, and
(2) indexes, indexes, indexes.
Also, I saw a reference to an article just the other day that discusses they pros and cons of putting all your (related) data into one table vs. splitting into smaller, sorta 'reference list' tables. I did not read it, and don't recall specifically where it is, but if you think this might be helpful, let me know. I'll try to dig it back up. (I think I saw the reference in one of the MySQL references).
Good job on the upgrades....I HAVE noticed a difference.
Though to be honest, most of the big bottlenecks I've noticed in the past have been due to pulling up banners from OUTSIDE sources (not your own in-house hosted banner images). I guess there's some things you can never control.