while (<DATA>) {
    if ( /\d{4}-?(\d{3})\s{0,}?(\d\d:\d\d:\d\d)?/ ) {
        print "Match: $_" ;
    } else {
        print "NO MATCH: $_";
    }
}

__DATA__
2005-100 10:12:01
2005100 10:12:01
2005-100
2005100
2005
[download]

That only prints "NO MATCH" on the last line of input, and to fix that, you just need one more "?" in the regex:

/\d{4}-?(\d{3})?\s{0,}?(\d\d:\d\d:\d\d)?/
#              ^--here
[download]

(updated code to fix indenting)