PHP: 7,261,540 Domains, 1,043,328 IP Addresses
Source: Netcraft
There has been some shakeout in the large-scale shared hosting space related to the .com crash and combined with some routing issues in Germany which caused 5-10% of German servers not being able to respond to the Netcraft queries. This hurt the PHP total domain numbers a bit in recent months, but they appear to be back up nicely as of the November and December numbers.
You can also see how popular PHP is relative to other Apache modules at . Spoiler: PHP is the most popular.