when using Universal for a return flight to the US, someone dropped the ball as far as customs notification, and we sat on the ground at Wilmington, NC, for an hour while waiting for the customs officer to show up. He had with him a fax, showing an incorrect arrival time.
I've been using Jeppesen JAS and jetplan.com. JAS works the best for multiple flightplans, jetplan works best for running updates for flightplans already run on JAS since you have the ability to recall JAS plans.
Have used GDC, Jepp JAS, Universal, and Air Routing.
My favorite for domestic ops is GDC. JAS is becoming more reliable however there are simply more options with GDC.
The best I've used for International ops is Universal. Although we like to trust our international handler's respective ADCUS systems, our SOP is to always call US Customs personally on the day of arrival in order to confirm our appointment with the agent. It saves time and embarassment... If we will arrive after hours, we call during normal business hours and get an after hours contact number for the agent assigned to us. They don't mind at all if it keeps things running smoothly.
I highly recommend www.fltplan.com for domestic flying.
It already has preloaded performance for a lot of aircraft, and you can further customize for the type of flying you do. Support is excellant and quick if you have trouble. It is also very quick. It does take a little setup though. I have mine customized to have my flight times within 2-3 minutes of actual and Fuel burns within 200-300 pounds of actual as well.