Multiple multisites?

So here’s a complex thought: Is is possible to have multiple ways to structure multiple domains for WP?

For instance, some sites would be structured as subdomains, and other ones on separate domains?

Also, if I incorporated other software into my overall site, but used a subdomain, would that create any potential conflict?
ie.
AuctionSoftware.MySite.com

And one last question that I can’t figure out. If I have several sites on different domains I manage using MU, would that mean users can have one login for all sites? I was under the impression that this isn’t possible to do.

Thanks! I’m planning to migrate my site to WP, but it’s a network of sites setup in a rather complex way, so I’m wondering if I’m going to break a whole hell of a lot of things from this migration.