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 a couple of other non-standard rules:
Automatic intentional walk: A batter can be intentionally walked by simply waving him to first base. The pitcher doesn't have to throw any pitches. One side effect of this rule is that it takes away the possibility of a balk, stolen base, or passed ball when an intentional walk is issued.
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.