Clicking noise

I recently bought a 1997 ES 300, V6 3.0 liter 150,000 miles. Though the car handles great, there is a clicking noise whenever the engine is running. I took it to a dealer and they said it had to do with my valvetrain. The unfortunate thing is that they didn't tell me anything else useful besides that it would cost $3000 to fix it. Though I do know that I could shop around for a lower price, I was wondering if it's something major, or simply an annoyance, also I was wondering would it be better to either rebuild/replace the engine and be more cost effective.