I can't give you definitive answers, but I'll make a start.
1. You are correct, if you click the printer button above the glossary, you get the glossary parsed in clean page format for printing. As for the other resource pages, what degree of friendliness do you prefer? The resources do all print and because Moodle is a simple interface, not much appears at the top or bottom. I'm thinking of a "printer-friendly" page from an online newspaper or something...most of them seem to have breadcrumbs or footer/headings, too. If you experiment on a moodle installation, you can create pages and then print them (feel free to use demo.somewords.org--though the link probably won't be alive forever). My suggestion would be that if you wanted them to appear differently, maybe you could make a feature request in the bugs.moodle.org tracker. Just be clear about what you would want the pages to look like. Often, it is helpful to the developers to work from a mock-up of what others want to see.
2. Since the search is on for a Document Management System
that can be integrated into Moodle, I don't expect a great deal of changes to occur in the resource module right away. I suspect that PDF and printer-friendly generation would be great features to look for. Right now, eyes are focused on OWL
as a potential candidate, you might check to see if it has those features. If not, perhaps you might uncover another good candidate that does have the features. This kind of research is really helpful in moodle.org.
3. Many of us use forums as a simple way for a class to create lists of student-discovered links (because of the subscription function, the email potential already exists); but moodle.org just started a handy glossary of links which might work for you, too (though it doesn't have an email function).. And yes, the dialogue has a toggle that allows all of the private messaging between two people to be duplicated and sent as email as well.