I was just thinking about this last night! I run multisite on nginx.
The thought I had was using defines in the config to separate theme files and blogs.dir to directories of your liking, then mapping a unique vhost for themes and a unique vhost for blogs.dir.
You could do the same for a single install with apache. You probably don't even need to move your themes or uploads to different directories, that's more of a personal preference.
The plugins look apache good.
Glad to see this list back on track!