Size of team roster? Pitching rotation? DH? Rules for substituting players (i.e. can someone come back into a game after subbing out, as in Little League?)? Other differences in the game?

These sites will help you out.
http://mlb.mlb.com/NASApp/mlb/mlb/offici...
http://www.answers.com/topic/baseball-ru...

NUMBER OF INNINGS

Innings length of feild innings pitched per game

Besides what's already been mentioned, high schools also allow the use of aluminum bats - in the majors, only wood are allowed.

The National Federation of High Schools bases its rules on those of Major League Baseball, the American League in particular, as they allow the designated hitter.

There are certain exceptions to those rules, which can be found in the NFHS rule book (you can order the book at their website www.nfhs.org, but they don't have it posted there). The biggest of those are rules allowing alumimum bats (within certain exit speed ratios), limiting a regular game to seven innings and rules allowing a player to re-enter a game one time.

Otherwise, the size of the field is the same and there are no rules limiting the number of pitches or innings thrown (although individual states may implement these if they deem necessary).