Troubleshooting Internet connections

We have servers co-located at NAP sites across the country and have several thousand users connect to us daily. When the users have packetloss or latency problems I have been using traceroute and ping to troubleshoot their connections. From some recent threads here, I am concerned that these tools are giving me a false image of which routers are having problems because of the differences between the way some routers process the packets sent to them and packets sent through them (different priorities and input queues). Is there anyway other then traceroute and ping to pinpoint problems on an Internet connection? Thanks for any ideas you may have. Wayne Hall Network Manager VIE