I noticed most directories insist any site submissions be root directory only (www.example.com).
What if I wanted to submit www.example.com/subdirectory/ as my listing? Would this be added or disregarded? If I already have a root directory listing, could this potentially get my existing listing removed?
Most directories have submission guidelines, and these vary widely. There are even a handful which will only list deeplinks. However, a lot of general directories stick to the rule that they will only list the root url, unless you pay. It makes sense if you know how many people try to spam and abuse the system.
I've found that Quadrille is right about directories with loose submission guidelines. There are a few out there that seem to list all comers, but you will be amongst 40 other sites on page 253 of a deep category in a lot of these cases.