You can unpack without java. The jdk comes with a native unpack program, which can be used by installers. The jre installer uses this technique (afaict).
http://java.sun.com/j2se/1.5.0/docs/tooldocs/share/unpack200.html
You could use these cmd line parameters:
pack200 --no-gzip --modification-time=latest --effort=9 --deflate-hint=“false” --strip-debug --unknown-attribute=strip foo.jar.pack foo.jar
http://java.sun.com/j2se/1.5.0/docs/tooldocs/share/pack200.html
And instead of gzip you could use a superior compression scheme like lzma. Over at 7.zip.org you can get the lzma sdk, which comes with a cmd line compressor/decompressor.
However, the best option would be using an installer, which already does that like NSIS.
With lzma the JEmu2 jar gets down to 201,947 Bytes (-fb255) and the rt.jar gets even down to 3,543,040 Bytes gasp
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Uhm yea… basically what Cas said. LZMA ftw! ;D