Hi Lukas,
So, yes. Everything you want to do there is possible.
- create a custom folder type is exactly the same as a custom content type except that you will set your type parent as cm:folder instead of cm:content
- I don't really understand what you call "reference to". If it's just having a link, add an "association" to your custom type and you are good!
- For the emails and attachements, you might want to setup alfresco's imap. It will enable you to directly drag and drop mails from your inbox instead of having to save your email and then upload it to alfresco.
Also, one thing you might want to look into is wether it would be suitable to use sites instead of just folders for "projects".
If it's just some document archiving, you can keep it as a folder.
If you have some collaboration work involved, you might want to create it as a site and benefit from the discussions/wiki/calendar/etc. that comes with it.