It all depends on how you define "best". I would assume that you really mean video conferencing software and not webcam software.
For multi-point conferencing Cu-SeeMe is still probably the best. Netmeeting is ok but the video codec it uses is not the best and microsoft is not really maintaining it anymore. And yes, netmeeting will work without messenger. There are a number of other video conferencing programs available, the best thing you can do is just try them out to see which one you like the best. Some of the other ones you might want to try are: ICUII, iVisit, Anywebcam, ISPQ, and CuSeeMeWorld. You can just do a search for other video conferencing programs.