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added 15 characters in body
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Finally I got it: Add this to your .bash_profile

function foomagick() {
    ls /Applications/ | grep "\.app" | grep -v iWork | while read APP; do
        # clean it up                                                           
        a=`echo $APP | sed s/\ //g`;
        a=`echo $a | sed s/\'//g`;
        echo alias ${a%.*}="'open -a \"${APP%.*}\"'"
    done
}
foomagick > foomagick.tmp
source foomagick.tmp
rm foomagick.tmp

Now the following work:

Skim # open Skim.app
Skim foo.pdf
FireFox http://google.com
FireFox google.com # ERROR. Looks for local file.
user588