I haven't used File::BOM, but I gather it will only work if the input data actually contains a byte-order-mark character (in fact, if it begins with said character); assuming this isn't true of your data, it won't help you much.

To elaborate on the first reply (which is basically correct, if you are in fact only deciding between Latin-1 and utf8), check the section about "Handling Malformed Data" in the Encode man page: basically, use the "decode" function like this:

#!/usr/bin/perl

use strict;
use Encode;

die "Usage: $0 latin1.file > utf8.file"
    unless ( @ARGV == 1 and -f $ARGV[0] );

open( my $fh, "<", $ARGV[0] ) or die "$ARGV[0]: $!";
{
    local $/;
    $_ = <$fh>;
    close $fh;
}

my $utf8;

eval { $utf8 = decode( "utf8", $_, Encode::FB_CROAK ) };

if ( $@ ) { # input was not utf8
    $utf8 = decode( "iso-8859-1", $_, Encode::FB_WARN );
}
binmode STDOUT, ":utf8";
print $utf8;
[download]

If you have to decide between utf8, Latin1, Latin2, Cyrillic, Greek, etc, then you have a harder job: to the extent that the non-Latin1 encodings use the same 8-bit range as Latin-1, Encode will happily pretend that they are all Latin-1, thereby converting them all to the wrong set of utf8 characters.

Encode::guess probably won't help you in that case -- you need to train up some bigram character models for each language... (well, maybe the Lingua branch on CPAN has something to handle this by now).