Ruby 35.3%
Python 11.5%
Javscript 9.4%
PHP 7.6%
C 5.4%
None 5.3%
Java 5.3%
C++ 4.0%
Objective C 3.8%
Perl 3.6%
C# 1.7%
Erlang 1.4%
ActionScript 1.3%
Scala 1.0%
Lua 0.9%
Clojure 0.7%
Lisp 0.6%
Haskell 0.5%
Go 0.5%
Objective J 0.3%
Pretty close to the overall estimate by github. Some of the difference can probably be explained by the fact that Github tried to eliminate commonly included libraries when they did their file line counts, while I didn't.I understand what you trying to do by eliminating projects with less than 4 watchers but this is arbitrary figure and the results you produced are therefore affected by this decision.
When you play with population samples then side effects can creep in. You can see this in the difference in Ruby being 35.3% in your figs and it being 21% on Github. Its a big difference and can possibly be explained by things like: http://www.ruby-toolbox.com/
Interesting to see how the Perl community has really hopped on the bandwagon. Happy to see it.
When I started my Github account in Nov 2008, Perl only had around 1% of language metrics. It rose over the past year to 6% and recently jumped to 14% because of the BackPAN inclusion (http://github.com/gitpan/).
Interestingly the latest language stats from GitHub (http://github.com/languages) shows this: