I may be missing something but I'd really like a file skip list option. Something for both uploads and downloads though maybe separable. Regex capable would be lovely.
1. Filters Select the Filters option from the Toolbar or Listing menu. You can choose to exclude (or only include) files / folders depending on name matches - Name is, Name is not, Name ends with, Name doesn't end with, etc.
2. Exclusions Select the files/folders you want excluded from the Sync then right-click (or control-click) on one of the selected items and from the menu that appears select 'Exclude -> Synchs'
Note that you will usually want to exclude the same items on both the Mac and Server sides, but this isn't enforced.