Out of these many thousands of ISP's there are only a handful which operate extensive high-speed backbone networks. Most other ISP's derive their connectivity from the larger ISP's.
Many ISP's interconnect with each other at Network Access Points (NAPs) It is at the NAP's that the end-user traffic from ISP#1 can transfer over to ISP#2 to reach a host computer/network which happens to be connected to ISP#2. Most recently, the top 4-5 ISP's (UUNET, MCI, SPRINT, BBN, ANS) have begun to increase the amount of "private peering" they do between themselves and a few of the other ISP's. These providers have several T-3 connections dedicated to inter-connecting their backbones without going through the NAPs.