Well, that is a complicated question because even though what you see is different, the underlying code to support these is the same. But to answer this as simple as possible. I recommend following this:
The pro is that when adding a custom field over using the Custom Fields is that the custom field is also automagically available in both the Form and Link addons whereas the Custom Fields is not. The con is the inverse.
Hope that helps!
ps. The confusing terminology lays with WordPress because WordPress pages and posts have a Custom Fields metabox too, but, at the same time they can have custom fields added by thems and plugins (ex. theme options for pages or posts). Clear as mud?!?