I have a unique problem, which is that I have installed my wordpress to a subdirectory, and symlinked httpdocs from several subdomains to that directory. The structure looks like this:

httpdocs/wp/ -> WP Install
subdomains/gadgets/httpdocs/ -> /elliottback.com/httpdocs/wp/
subdomains/books/httpdocs/ -> /elliottback.com/httpdocs/wp/

This means that from my domain, we’re always sticking an extra /wp onto things, but from the subdomains, they go directly into the wp-content directories from the root , in both relative and absolute sense. I consolidated my subdomains this way so that I could run a single WP install and maintain them together. Here’s the .htaccess file that lets WP Super Cache work on either of them:

# BEGIN WPSuperCache
<ifmodule mod_rewrite.c>
RewriteEngine On
AddDefaultCharset UTF-8
RewriteBase /
RewriteCond %{REQUEST_URI} !^.*[^/]$
RewriteCond %{REQUEST_URI} !^.*//.*$
RewriteCond %{REQUEST_METHOD} !=POST
RewriteCond %{QUERY_STRING} !.*=.*
RewriteCond %{HTTP:Cookie} !^.*(comment_author_|wordpress|wp-postpass_).*$
RewriteCond %{HTTP:Accept-Encoding} gzip
RewriteCond %{REQUEST_URI} ^(/wp)?/
RewriteCond %{DOCUMENT_ROOT}%1/wp-content/cache/supercache/%{HTTP_HOST}/%1/$1/index.html.gz -f
RewriteRule ^(.*) %1/wp-content/cache/supercache/%{HTTP_HOST}/%1/$1/index.html.gz [L]

RewriteCond %{REQUEST_URI} !^.*[^/]$
RewriteCond %{REQUEST_URI} !^.*//.*$
RewriteCond %{REQUEST_METHOD} !=POST
RewriteCond %{QUERY_STRING} !.*=.*
RewriteCond %{HTTP:Cookie} !^.*(comment_author_|wordpress|wp-postpass_).*$
RewriteCond %{REQUEST_URI} ^(/wp)?/
RewriteCond %{DOCUMENT_ROOT}%1/wp-content/cache/supercache/%{HTTP_HOST}%1/$1/index.html -f
RewriteRule ^(.*) %1/wp-content/cache/supercache/%{HTTP_HOST}%1/$1/index.html [L]
</ifmodule>
# END WPSuperCache

Let me know what you think–performance stats show that it’s working fine for both the /wp subdirectory and the other subdomains!