In terms of funding academic research, I think there's good reason to think that funding think tanks is probably best. Specifically, let's talk about George Mason University, the Kochs, and the Mercatus Center. Researchers are cheap to support, and by having one particular home that attracts many ideologically similar people, you get additional useful social networking effects that you might not get if you just gave some grants with the money. (Go down the Mercatus Center fellow list, and you'll see some familiar names like Robin Hanson and Tyler Cowen and (if you're libertarian / into open borders) Bryan Caplan.)
Researchers are cheap to support
Humanities researchers. Supporting, say, a high-energy experimental physicist can get quite expensive X-)
Many of the biggest historical success stories in philanthropy have come in the form of funding for academic research. This suggests that the topic of how to purchase such research well should be of interest to effective altruists. Less Wrong survey results indicate that a nontrivial fraction of LW has firsthand experience with the academic research environment. Inspired by the recent Elon Musk donation announcement, this is a thread for discussion of effectively using money to enable important, useful research. Feel free to brainstorm your own questions and ideas before reading what's written in the thread.