Here is my issue, I am selecting and doing multiple joins to get the correct items...it pulls in a fair amount of rows, above 100,000. This query takes more than 5mins when the
Try adding indexes on the fields that you join. It may or may not improve the performance.
Moreover it also depends on the engine that you are using. If you are using InnoDB check your configuration params. I had faced a similar problem, as the default configuration of innodb wont scale much as myisam's default configuration.