For starters, a good system for NAT (Network Address Traversal) and routing, to combat any woes with firewalls and proxies. PC gamers should never have to deal with forwarding ports or anything similar.
Even better: An open-source, distributed multiplayer game network (eg. Battle.net, Xbox Live, PSN...). This would essentially be a protocol that anyone can implement, and anyone can run a server - they just communicate with each other to pass around information about who can be found where. Similar to distributed social networks (eg. Diaspora), this keeps any one party from having control, whilst allowing any indie game to seamlessly integrate into it.
Imagine if you could just add your friends as 'friends', and then any game you ever played you could just invite them straight away, no ip addresses, no id lookups, you just take them with you. Basically what B.net/XBL/PSN do already, but open and free for all!