October 1999: 931122 Domains, 321128 IP Addresses
Source: Netcraft

Note: We do not know what caused the sudden surge in the number of domains and then the subsequent drop-off. The number of physical servers actually running PHP has ben growing steadily as witnessed by the steady climb in the number of unique IP's identifying themselves as being PHP servers.

One possible explanation for the domain bubble is that a couple of large ISP's switched from running the module version to the CGI version. Servers that run the CGI version of PHP are not reflected in these stats.

You can also see how popular PHP is relative to other Apache modules at E-Soft Inc.'s web survey. (Spoiler: PHP is the most popular)