Had this same thing happen to me...

Server error codes kept pointing to /mysite.com/.htaccess RewriteBase: .........

Now my answer might be a little noob, but, I figured I would share it anyway cause I'm sure it will pop up again.

My error came upon editing the .htaccess in the Artio SEF component while in my joomla backend. Once I saved the .htaccess my site instantly returned the dreaded: Internal Server Error 500. In a panic I went in and manually turned of SEF operations in my joomla configuration file. No change, I then went in and manually disabled the component in its configuration file. Still no change. Now at this point my site is useless, Internal Server Error frontend, backend, and nothing is happening. I read volumes of htaccess references until I finally came to the conclusion that the htaccess.txt file I had should with all reason work just fine.

The one thing that could've saved me the time and aggravation; was remembering to rename htaccess.txt to .htaccess! note: I just grabbed a working htaccess.txt file from one of my other installations, uploaded it to my server, renamed it, and voila!

Once I did that my site was back in action. Now that may or may not be what's happened to you but the amount of sh@t I went through you'd think there would be a little more emphasis on that kinda thing. Again, probably a noob oversight but I've been up all night and I'm tired as hell and needed to rant about it somewhere.

Hope that helps somebody!
Goodnight