Some things I'd like to see in a unified online open system:
* Hyperlinking between papers
* Discussion threads for papers
* Collaborative mark ups of papers, so that difficult papers can be communally dissected and fleshed out, or so that students can work through a paper and provide a mark up to ease the reading for other students
* An ongoing wiki for every subfield, detailing current outstanding problems, papers to read to get up to speed, most recent progress, etc, as well as curating accepted knowledge. Wikis should also be able to be marked up by students, so that difficult material can be broken down and fleshed out for the sake of other students.
A great example of moving in this direction is the recent P=NP discussion that happened largely on Dick Lipton's blog (http://rjlipton.wordpress.com/2010/08/08/a-proof-that-p-is-n...).
edit: I partially take-back my suggestion of Faculty of 1000. Apparently, they are not open to unaffiliated and require a subscription. I like what they're doing, but it shouldn't be so ivory-toweresque.