use strict;
use warnings;
use File::Basename;
use Text::ParseWords;

# I moved your sub to the bottom. I guess that's a matter of personal taste,
# at any rate I like it better that way.

# I included this line so we get to call getValue without parens or that
# ugly &sigil.
use subs qw(getValue);

# Three-argument open() is generally preferred.
# Also, file handles can go into scalars and that's actually the
# recommended way to go about things these days.
# Error checking for opening now happens right after the attempt to
# open # the file, instead of after the while(){} block.
open my $file, "<", $ARGV[0] or die "Couldn't open file '$ARGV[0]': $!.\nDid you specify a valid file?";


# I've moved the three variables here, so that we don't lose their
# values through iterations.
# Also, why are you using arrays when they clearly work as scalars?
# I changed that.
# my (@ID,@ISIN,@SYMBOL);
my ($ID, $ISIN, $SYMBOL);


# Fixed indentation.
# Also, I usually don't like working with $_.
# There's too many subtleties and pitfalls.
while (my $line = <$file>) {
        # I don't care about newlines
        chomp $line;

        if ($line =~ m/ID:/) { $ID = getValue $line ; }
        if ($line =~ m/ISIN:/) { $ISIN = getValue $line ; }
        if ($line =~ m/Symbol:/) { $SYMBOL = getValue $line; }

        # When all of $ID, $ISIN, and $SYMBOL are set, we can
        # print this stuff.

        if (defined($ID) and defined($ISIN) and defined($SYMBOL)) {
                # You wanted a newline, right?
                # Okay, I'll give you a newline!
                print "$ID:$ISIN:$SYMBOL\n";
                # There it is ----------^^

                # You still prefer to go with printf? Okay.
                # printf "%s:%s:%s\n", $ID, $ISIN, $SYMBOL;

                # And reset the stuff.
                undef $ID;
                undef $ISIN;
                undef $SYMBOL;
        }


        # Same thing here - you just want a scalar that holds all the
        # values. But do you really need it? I don't think so.
        # my @FULLVAR = (@ID,@ISIN,@SYMBOL);
        
        # Same goes for these - what are these sweeties doing here?
        #my $num = 0;
        #my $count = 0;

        # I'm not even sure what this is supposed to do,
        # or why you use printf but none of its formatting capabilities.
        # Also, we've moved the printing part to inside the new if(){}
        # block so I'm gonna comment this out.
        # foreach (@ID,@ISIN,@SYMBOL) { printf  "$_:"; }
} # This curly bracket ends the while(){} block...

# But then what's going on here?
# I'm guessing it's a copy-paste error, because I get an error:
# Unmatched right curly bracket at ...
# Also, we've moved this piece to the line where we try to open the
# file, so begone with it!
#} else {
#        print "You need to specify an input file \n";
#        print "Usage : ".basename($0)." difffile.txt \n";
#        exit;
#}


sub getValue {
        # Are you sure this regular expression is correct?
        # It removes all spaces, but in the example you provided
        # you showed that you wanted to keep the space in the
        # Symbol field.
        # $_ =~ s/\s//g;

        # My guess is that you just want to trim leading and trailing
        # spaces from the value, so let's do that. And where would these
        # spaces occur? Right after the colon, so let's make it part
        # of the string to split on.

        my $line = shift;
        
        my ($name, $value) = split(/:\s*/, $line);
        chomp $value;
        return $value;
}

##</code><code>##

G:\>perl x.pl

G:\>perl nonexistant.pl
Can't open perl script "nonexistant.pl": No such file or directory

G:\>perl x.pl diff.txt
QYQ:SE0004017929:LUP2L 100OHM
R1M:SE0004018539:TLS2K 50OHM
QNF:SE0003990183:MINILONG OMX A O
QX8:SE0004017440:ALF2K 160OHM
NC0:SE0003842137:BOL2K 170OHM
NEV:SE0003843069:NOK2K 90OHM

G:\>