I auto-upgraded about 3 minutes ago and got this error when I refreshed my site (http://theagnonschool.org):

WordPress database error: [You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'order ASC' at line 1]
SELECT t.*, tt.* FROM wp_terms AS t INNER JOIN wp_term_taxonomy AS tt ON t.term_id = tt.term_id WHERE tt.taxonomy IN ('category') AND ( t.term_id <> 1 AND t.term_id <> 9 AND t.term_id <> 46 AND t.term_id <> 48 ) ORDER BY order ASC

And, OK, I was an idiot. Because every other upgrade I've done has gone super smoothly, for some reason I thought it would be OK not to back up (although I do have autobackups from yesterday).

So then I tried:
Reinstalled the earlier the previous version of WP. Still got the error message.
Restored my database to a version from a couple days before the upgrade. Still got error message.
Repaired my database from cPanel. Still got error message.
Tried again to upgrade to 2.8.3. Still got error message.

I don't know anything about MySQL. I did sent a support ticket to my host, Hostgator, and posted the problem on the Auto upgrade 2.8.2 to 2.8.3 "Installation Failed" forum at WP.org.

It doesn't seem that likely to me that Atahualpa is involved in the problem at all, but please, does anyone have any ideas about what went wrong or suggestions about what I should do?

I just heard back from Hostgator:

Greetings and Salutations!

Looks like this was caused by the my-category-order plugin. I moved the directory (/home/shem/public_html/wp-content/plugins/my-category-order/ to /home/shem/public_html/wp-content/plugins/my-category-order.old) and this resolved the error at the top of the screen. I went and downloaded the newest version of WordPress but was still getting this error. It seems this part of the query "ORDER BY order ASC" is incorrect (where oder ASC needs to be tt_order ASC or something similar).

In the mean time, the website is no longer displaying any errors, but you may want to get a hold of the plugin author to resolve this issue. Youc an more information here:

http://wordpress.org/extend/plugins/my-category-order/

Hope this helps! Please do not hesitate to contact us if you are in need of further assistance.

Have a wonderful day!

So this is resolved, but anyone else who uses My Category Order might want to beware when upgrading.