I refactored a slow section of an application we inherited from another company to use an inner join instead of a subquery like:
WHERE id IN (SELECT id FROM
before the queries are run against the dataset they are put through a query optimizer, the optimizer attempts to organize the query in such a fashion that it can remove as many tuples (rows) from the result set as quickly as it can. Often when you use subqueries (especially bad ones) the tuples can't be pruned out of the result set until the outer query starts to run.
With out seeing the the query its hard to say what was so bad about the original, but my guess would be it was something that the optimizer just couldn't make much better. Running 'explain' will show you the optimizers method for retrieving the data.