Here's one simple way.

use threads; use threads::shared;

my @file1 : shared;
my $t1 = async{
    my $getfile1 = qq/getS1config.pl/;
    open (FILE1, "$getfile1 |" );
    @file1 = <FILE1>;
};

my @file2 : shared;
my $t2 = async{
    my $getfile2 = qq/getS2config.pl/;
    open (FILE2, "$getfile2|" );
    @file2 = <FILE2>;
};

my @file3 : shared;
my $t3 = async{
    my $getfile3 = qq/getS3config.pl/;
    open (FILE3, "$getfile3 |" );
    @file3 = <FILE3>;
};

$_->join for $t1, $t2, $t3;

## Do stuff with the arrays.
[download]

Note that assigning single scalars into arrays in order to interpolate those scalars into strings is a very dubious practice. You should also be checking your opens and much else. You will have to use lexical variables to use :share

This is a minimal demonstration that could be much improved.

What is the best way to run several commands simultaneously? I have a script that calls many other scripts which load different files into arrays, they run sequentially which takes several minutes, ie:

First of all, are you sure that you will have an advantage parallelizing these tasks? The fact that you write that your other scripts "load different files into arrays" suggests, without further specifications, that these files are local ones, and if so then parallelizing won't buy you much.

Also, usage of single element arrays for interpolating and unchecked opens apart, your code is not much different from a series of do EXPR statements, and although I'm not particularly fond of this technique, it is at least less verbose, so you may want to go that way instead.

One particular problem that I see with your code is that you have these getS1config.pl, getS2config.pl, etc. scripts which bear very similar names: I know that a priori this means nothing and that they could actually be wildly different, but isn't it that by any chance they're very similar instead and could be factored away in some code that you may include in your main script, without the overhead of having to start additional processes, and in particular perl interpreters?