Are there universities and labs that are unaffiliated with the Tor Project that are researching Tor and Onion Routing and contributing back to the Tor Project (be it in code, security audits, or just publishing papers about how Tor could be made more secure)?
If so, what labs are out there and what concepts are they researching (and where is there funding coming from if that information is available)?
Yes!
We made a small list of groups that have known and recommended Tor researchers here: https://research.torproject.org/groups.html
But there are literally dozens of research groups working on evaluating and/or improving Tor. Take a look at http://freehaven.net/anonbib/ for all the good examples I've found so far.
As for where their funding comes from, it varies widely. Many of them (in the US) get funding from NSF. Some of them are European and get funding from various EU research agencies.
