Tor uses the SOCKS4a protocol, but most applications that have SOCKS4 support, as stated previously by others, don't quite use SOCKS4a and leak out DNS traffic. Privoxy is an http proxy to stick between the browser and Tor in order to alleviate that (and also filter out ads, http headers, etc).
On a side note, the Vidalia bundle that is available on the Tor website no longer uses Privoxy. It's considered outdated and unmaintained. The Vidalia bundle uses Polipo in its place.
Also remember that anonymity != confidentiality != 'security'.
In case you're curious, I've found a SOCKS proxy server called polipo. It says it supports IPv6 but not link-local addresses. I'm not sure if that means it will work for cjdns or not, but if you happen to have more knowledge on this and
Heh, I'll admit this question was out of ignorance of how some of this works. I think I'll devote a day to reading up on the underlying workings of this so I know what I'm doing. Thank you for the advice. :) I actually have two linux computers on the east coast a fair distance from each other that could act as nodes... so I feel like I could help a little at least?
I'll be honest, it was more a concern of overloading the network or something by somehow sending torrent traffic over it. But now I see that this isn't really the same thing, meshnet is it's own network but dependent on the "real" internet's infrastructure to communicate? I think I'm making more sense of this now, I thought it was just another network protocol that was more difficult to censor.
Would it be reasonable for me to assume that IPv4 traffic and IPv6 traffic are isolated from each other in this setup? I mean, unless I set up a server with an IPv4 address to work with IPv6... it shouldn't?
I see people have already covered the monitoring to diagnose the cause. That's good, because I don't know how. But I would also suggest trying a caching proxy such as Polipo. I don't know how much of an effect it would have--probably very little, really--but it may help a smidge.