We go through this at the lawfirm. In my department, the files are filed alphabetically by client name - last name for individuals; company name for businesses. Everything is put in chronological order with the latest on top. We have separate files for pleadings, correspondence, client documents, etc.

Some departments sort by client number, but I know everyone has the most recent stuff on top. Just makes it easier to file - can you imagine digging to the back to put the newest stuff in? That doesn't make sense to me.

Paperclips in files drive me nuts! It just makes the files thicker and more difficult to handle. If the document is meant to be kept together, it's stapled.