I have to comment that your use of semicolons as pattern delimiters rather obfuscates this - I had to look twice before I saw exactly what was happening. Rewritten in a more traditional fashion, and using chomp rather than a mapped substitution to get rid of newlines, it immediately becomes a lot more legible:

while (<STDIN>){
    chomp;
    print grep !$a{$_}++, split m/\s/;
    print "\n";
}
[download]

I don't see a whole lot of room for improvement there. There is not really any way to avoid the hash growing that large, as far as I can see, as you can't simply expire any of its items.

Makeshifts last the longest.