The kind of software you require is VERY complex. There is not really any free solutions that can manage what you require. All the information required to write your own solution is available on the internet. For qmail the book running qmail is quite usful (sorry dont have it to had so cant give author etc). As for apache and proftpd they are fairly easy to do. Its not that difficult to get your ftp and apache traffic processed and get summary information bunged into mysql. SMTP logging is a bit more complex but possible :-)
It also quite easy to do things like log per user webmail usage.
If you really want something to do what you require then I am afraid you would be better using a complete control panel solution, or writting it yourself!
Well, as for me... Apache & ProFTPD is not a problem. It was very easy. Get a webalizer - free log analysis package. You can use it to track traffic (for example by a domain or by user) for apache and (the easiest variant: by user) for ProFTPD. Traffic counting for qmail - I think that is possible too but... Have never implemented it. One of variants is to add some calls inside of qmail launching your own script when the mail is received and should be stored in queue (for local delivery) and when the mail will be routed to outbound SMTP delivery.