About this site
The courtesy runner is a non-standard rule of baseball. It is used in high schools in some US states, and some tournaments, but the primary user is the NAIA (National Association of Intercollegiate Athletics), and NAIA baseball is what this site is about.
The courtesy runner rule allows a team to substitute (as in, send in a pinch runner) for a catcher or pitcher whenever a catcher or pitcher reaches base, without the catcher or pitcher leaving the game. The idea, as far as catchers is concerned, is to speed up the game; the catcher can return to the dugout and put on his chest protector and shin guards. For pitchers, well, I guess the idea is to keep pitchers off the base paths, but since the NAIA allows designated hitters, this use of courtesy runners doesn't come up very often.
The NAIA uses another non-standard rule, the re-entry rule; A starting position player may leave and re-enter the game once. When he re-enters, he must take the same spot in the batting order. Pitchers and designated hitters cannot re-enter.
The NAIA used the automatic intentional walk for many years before it was adopted by all of professional baseball, and NCAA Division II and Division III. The NCAA is considering adopting it for Division I.