This handy set of rules for mod_rewrite automatically redirects any URL ending in "/index.php" to the same URL ending in "/."  It works for the root directory as well as subdirectories.

RewriteCond %{THE_REQUEST} ^GET\ /.*/index\.(php|html)\ HTTP
RewriteRule (.*)index\.(php|html)$ /$1 [R=301,L]

For example, "http://www.example.com/subdirectory/index.php" would be redirected to "http://www.example.com/subdirectory/."

This eliminates one of the peskier canonicalization issues with relative ease.  It's a bit tricky because of the way mod_rewrite updates its variables during execution — hence the odd use of the variable {THE_REQUEST}.  If anyone knows an easier way or finds a problem with it, leave a comment. 

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Excerpt: I've seen many misconceptions about mod_rewrite.  I believe this is because most people in this industry know what it is, but aren't programmers, or don't understand the concepts well. First, I've seen people say mod_rewrite incurs major overhead. This may be true if you ask apes to write your regular expressions, and all of your expressions are PT (pass through) and execute every other expression in the list, so I don't know where that came from.Then there are the other people who think mod_rewrite is a revelation from God, a sort of third testament between SEOs and a higher entity.  This…