If you use JDK6 for development and
testing then
you should say JDK6 in your version.txt file. Of course JDK5 is also ok but if you used any JDK6 methods (especially in Swing) then running in JDK5 will not work.
Personally I don't know if JDK5 has obsoleted or not. So I recommend using JDK6. You may want to check Sun's JDK end of life page if JDK5 is outdated or not. Ok just checked
J2SE 5.0 is in its Java Technology End of Life (EOL) transition period. The EOL transition period began April 8th, 2008 and will complete October 30th, 2009, when J2SE 5.0 will have reached its End of Service Life (EOSL).