I'm using Atahualpa 3.6 and WP 3.0.4 with Godaddy hosting. The site has worked fine up until today with no changes and now I get the 500 Internal Server Error. I can access the backend fine but can't figure out why it's not working now. Godaddy says it's a theme issue but I dont' buy that since it's worked in the past and I have other sites that are working fine as well. The only thing is that other themes do work. I also turned off all plugins to no avail. Any thoughts? Thanks.

this could be a .htaccess file error or you might have the suhosin error.
can you get into the backend.? If so go to the permalinks and switch to the default and see what happens.

If you can't get into the backend, FTP to the site and go to the wp-content/themes folder and rename the atahualpa folder to something else and go into it and rename index.php to indexold.php. Doing this should force WordPress to switch to the default Twenty-ten theme and your site will be back up.

Then I would manually install 3.5.3 and 3.6.4 and look at the 'Suhosin' thread

I've been having the same issue with godaddy since yesterday. They are "working on it" but they don't seem to know what the problem is. My page won't load and I get this message:
IIS 7.0 Detailed Error -- 500.0 - Internal Server Error.

I can't find my .htaccess file on godaddy to make the suggested changes. Any ideas on where to look? Thanks!

did you ask goDaddy what they did yesterday? (What changes they made?)

I'm having the same issue with GoDaddy. Atahualpa 3.6.4 and WP 3.1
Everything has been working fine... until today. No changes on my end. This has been a static page for months. Now I get the 500 internal server error. I can login to the backend. If I switch to a different theme it works fine, but when I switch back I have the same results. GoDaddy has said that nothing changed on their end.
I'll try reinstalling the theme tonight.

**Also, I have tried disabling all plugins, but it's had no effect.

I would ask GoDaddy what change they made to the server., cause if you didn't change anything and it was working, only a change on the server would explain this.