Here is a dump of all of my waypoints on my server. The ones I made myself:
ns_blackmesa_t003, ns_square_redux_t05, co_reactor, ns_supersiege004a, ns_canyon21xx, ns_canyon21xy, ns_machina, ns_lucid, co_umbra, co_poseidon, ns_nothing, ns_agora and the newest is ns_origin. ns_origin was one of the longer maps to waypoint (262 minutes or 4hr 36m, 767 waypoints, only beaten by ns_machina at 7 hours.)
The other waypoints are included because I don't know which ones I modified (I know I did some work on ns_hera.)
Take note of the *_str.cfg files and the included co_reactor. ns_nothing and ns_origin were modified with stripper2 to fix the elevators and make them return to the bottom of the shaft after waiting 2 seconds at the top. The reason I had to do this is because bots are unable to tell what state the elevator is in and will squish themselves frequently because of it. co_reactor was modified by both stripper2 AND ripent, so you need to replace your co_reactor with the one in the ZIP (don't worry, the clients won't have to redownload it.)
tl;dr, you MUST have stripper2 plugin (which can be downloaded from botmans site) running on your server or the bots will not be able to navigate the level correctly.