As far as temporarily relief, I like a cream/gel called BioFreeze. It was recommended to me by a physical therapist, and I have to say it has been much more helpful than BenGay or AsperCreme. You can purchase it on Amazon.com.
I also get trapezius pain when sitting for a long time at my desk. You may want to get up every 30-60 minutes and do 2-3 minutes of stretches to keep yourself mobile. Below are some youtube videos with exercises/stretches that may help: