In larger scripts, I simultaneously handle that and the clarity issue by writing code like this

001 use IO::Handle;
002 STDOUT->autoflush;
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I got kinda turned off of IO->Handle when I read this comment in the pod

 use IO::Handle;     # thousands of lines just for autoflush :-(
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When I read the authors name, it strengthened the feeling.

Update: To clarify, the author to which I referred was the author of the comment I quoted above--from the pod of perlipc not IO->Handle--Tom Christiansen, who comments are to be valued.

I have absolutely nothing against Graham Barr (the author of IO::Handle), nor even much against that module.

My only reservation was of the practice of using IO->Handle only for the purposes of turning on autoflush.

If $|=1; $|=0; is deemed to cryptic, you could use something like:

sub autoflush (*$) { 
# Set the state of autoflush for 
# the handle supplied as $_[0] 
# to the boolean state supplied as $_[1]
    select( 
        do{ 
            my $old = select( $_[0] ); 
            $| = $_[1]; 
            $old; 
        } 
    ) 
}
...
autoflush( STDOUT, 1 ); # autoflush on
...
autoflush( STDOUT, 0 ); # autoflush off
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