It's all about quality unique content. The reason a lot of .edu's do well is because they have a lot of domain authority and a lot of them have been around for a long time. The directories that pass good link juice have this going for them as well. If you create a link farm on an .edu domain, you won't be fooling the search engines. It'll be a brand new site with no links to it that has no unique content which links out to a bunch of sites which may also be spammy, aka a link farm.
I'm not sure what your goal is with this site. If your goal in creating the site is to give an SEO bonus to these site you're linking to, I doubt it do any good. If your goal is to create a site that is a directory that is useful to people, and people start using it, linking to it, sharing it, then it could work. If your goal is to put up a site that has some links for your own enjoyment, go for it! If Google thinks your site is a link farm, it's not like they're going to dispatch agents to your house in the middle of the night or anything. 
