I ran into a problem when updating WP-Super Cache to version 0.8.9. I have two blogs on the same server, updated the plugin on both, and subsequently saw a massive drop-off in traffic on one site.
I discovered that it was actually showing a 500 server error on that site, but the other one remained typical. I checked both blogs, but they looked fine as far as I could tell. A little investigation turned up "ExpiresActive not allowed here" in the Apache error log. It was the new .htaccess file in wp-content/cache. The reason I hadn't seen the error myself was that I was logged in, so it wasn't trying to load from the cache.
The two sites had different AllowOverride permissions in the Apache config. One had "AllowOverride All", and was perfectly happy. The other had "AllowOverride FileInfo Options", which isn't enough for ExpiresActive.
I added Indexes to the AllowOverride line, and now the site seems to be back to normal. I figured I'd post the problem and solution in case anyone else ran into it when upgrading the plugin.