What does your data structure look like, when it's read into your program? If you have categories in an array, it's not too complicated:

while (@lines) {
    $output .= "<TR>";
    for ( 1 .. 3 ) {
        $output .= "<TD>" . (shift @lines) . "</TD>";
    }
    $output .= "</TR>";
}
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You might use the following to make sure you have an appropriate number of things in @lines:

my $fill = scalar @lines % 3;
while ($fill-- > 0) {
    push @lines, " ";
}
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