As a possible Rube Goldberg workaround, can't squid be configured to use a proxy itself? If so, and you want the various smart features of proxychains, you could run some other no-op proxy that works under proxychains. Maybe even an earlier version of squid installed in an alternate path and configured to do nothing:
squid-3.1 --> squid-3.0-noop --> proxychains
I.e. invoke proxychains /path/to/squid-3.0/bin/squid (with squid-3.0 configured to proxy request unmodified and listen on, say, port 12345), and then invoke squid-3.1 normally, but configure it to route all requests through localhost:12345.
It's convoluted, but it gets you the 3.1 features plus the proxychains features, at least until/unless some wiser soul figures out how to get it working directly.
You can manipulate the log output with the debug_options directive.
EDITED:
Something like
debug_options ALL,1 11,3 31,3 65,3
Refer to the cvs here
Best Answer
You will need to go with 3.1 if you want to proxy IPv6 traffic. Otherwise, I would install the latest version packaged for your distribution.