http://www.internetpulse.net/ and http://traceroute.org/ are two sites I used in addition to the usual unix tools like traceroute.

many providers also host "Looking glasess". Its a server hanging off their core network that allows you to run pings and traceroutes

http://lookingglass.level3.net/ (seems to be down currently)

a nice big list of looking glasses

http://www.lookinglass.org/

trace route is nice BUT mtr is better. Mtr does averages on latency at every node and any lost packets.