A solution is to prefix the program with ruby -S and jruby -S like
ruby -S rake
jruby -S rake
ruby -S gem list
jruby -S gem list
This way, we explicitly tell which interpreter we want to use and it will automatically find the right program in the right path. Problem solved.
If you want to install multiple Ruby vesions in the same machine, use MultiRuby as described in Dr Nic's Future proofing your Ruby code. Ruby 1.9.1 is coming.