If you have MySQL installed first, then the Apache port will detect it and use that version.
If you don't have MySQL installed, you can set WITH_MYSQL_VER=51 in /etc/make.conf, and the Apache port will pick that up and install the 5.1 mysql port.
If you don't have MySQL install, and nothing set in make.conf, then the default mysql version for the ports tree is 5.0.
Unless there's a specific feature in MySQL 5.1 that is not in 5.0, you should stick with 5.0. It's the fastest version of MySQL on FreeBSD. Kris Kenneway did a bunch of benchmarking with FreeBSD 7.x and 8.x on MySQL 4.x, 5.0, and 5.1 earlier in the year, and 5.0 was much faster than 5.1.
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