Mysql's full-text search engine is not very powerful and support comes only with Myisam engine. Sphinx is a full-text search engine replacement for Mysql and Postgresql. Also, It's possible to use Sphinx full-text search engine with both Myisam and InnoDB engines. You can read detailed information about mysql compilation with sphinx on Sphinx site.
I have faced with following error message, while compiling Mysql with innodb and sphinx engine support ( ./configure --prefix=/data/mysql3/ --with-plugins=sphinx,innobase). I used the innodb (base) which bundled with Mysql. You can also compile innodb plugin which has additional features. For example, on the fly compression, speed improvements.
configure: error: unknown plugin: sphinx
The trick was to run autorun.sh command in Mysql's source tree before running configure with sphinx engine support. This script will create a new configure script which knows how to compile sphinx engine.