Several decades a go I used a German temperature-compensated mechanical type altimeter to help navigate in the mountains for backpacking. I would calibrate it when I knew were I was on the topo. It was really very accurate. Better than a compass when you are in the trees. Many GPS units have an air-pressure type altimeter because of the poor altitude resolution of GPS. However, the new WAAS mode might be accurate. I understand that it will eventually be used for auto-pilot takeoff and landing of aircraft. If true, it might have very good altitude accuracy.
Today, I would calibrate my altimeter with a NOAA radio receiver. I found once a day was adequate.
As already commented, you do get GPS drop-outs in the trees, mountains and I would add, among tall buildings. But that's not too bad unless you are trying to generate/record a track. The benefit of a topo road map might make a GPS worth while. I think one of the new Garmins will give you the map ($100 extra), WAAS and 24 hours on two AA batteries. Not bad.
Al