If Schedule::Cron won't do what you're looking for (I suspect it probably will, but I've never used it), maybe you could use something like this:

#! /usr/bin/perl

use strict;
use warnings ;
use diagnostics ;

sub schedule (&@)
{
    my ( $condition, $exec_stmt ) = @_ ;
    if ( &{$condition} )
    {
        my $pid = fork() ;
        if ( !$pid )
        {
            exec( $exec_stmt ) ;
        }
    }
}

while ( 1 )
{
    my ( $min, $hour, $mday, $mon, $year, $wday ) = ( localtime )[1..6
+] ;
    $year += 1900 ;

    # Run everyday at 12:00
    schedule { $hour == 12 && $min == 00 } '/usr/bin/some/prog' ;

    # Run every three hours
    schedule { $hour % 3 == 0 } '/usr/sbin/some/other/prog' ;

    # Every Tuesday, plus the 1st & 15th of every month at midnight.
    schedule {
           ( $hour == 0 && $min == 0 ) &&
           ( ( $wday == 2 ) || ( $mday == 1 || $mday == 15 ) )
             } '/usr/local/bin/yet/another/prog' ;

    sleep 60 ;
}
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