W3TotalCache and Javascript — what should go where, when?

I’ve found that the best method is to do a view source then add the scripts to W3 in the same order they are listed in the source using the same url including the query string.

Most problems are from plugins or themes that output javascript inline. I try to move these to a custom.js file that is always listed last on W3.

If any scripts break when when minified either leave them out of minify or use combine only.