Best way to build a SMART mySQL & PHP search engine?

Ajreal is right...just thought I'd add an example to help out:

$query = sprintf("SELECT *, 
         MATCH(col1, col2) AGAINST('%s' IN BOOLEAN MODE) AS relevance
     FROM my_table
     ORDER BY relevance DESC LIMIT 20", $keyword);
$rs = $conn->query($query);

Hope this helps

like '%term%' is terrible slow and unoptimized , you might want to add full-text for this column, and use boolean mode for this

Such as

match(column) against('+One +Shop +Stop' in boolean mode)

Take note on the min word lengths is 4, so, you need to consider change it to three, and full-text search only available for myisam

Other opensource search engine like sphinx is ideal for this too