Did you optimize your queries? (eg add an index to your table for WHERE query match)
You should look at your select statements with the EXPLAIN (just add this in front of your select statement and run the query).
You could use a heap table, which takes up a lot of RAM, but is wicked fast.
You might also want to run myisamchk -r tablename (or OPTIMIZE TABLE tablename😉. There are other MySQL optimizations available with myisamchk...
Not sure if it applies in your case, but Zend has an accelerator (Zend Accelerator 2.0) which ups performance significantly.