We're using Confio Ignite to track query performance. It's the only tool I've seen with a strong focus on which queries that perform bad, and why. Recommended!
We're also using Quest Spotlight for our most important servers. For our not so important servers (if there are such things as not so important servers) we use a heavily modified version of SQLH2. We've stripped out some features and added some, and we've completely rewritten all reports in SQLH2 since the originals looked like sh*t.