When you set CPS (or Commands Per Second) in the games does it limit commands per player to what it's set at, per game, or per box?  Since it's a global setting, I'd assume the box, but would rather think it's per player.

It is a global setting and will effect all games.  If you set it to 10, it limits each player to sending 10 commands per cycle, which calculates to about a second.  This setting will effect some scripts more than others.  For instance, moving product from one planet to another will be considerably slower, however pdrop scripts won't be effected much since it will be sent in bursts and not continuous cycles.  Hope this helps.

Would you also have to take consideration with the number of games hosted when setting the CPS? I run 40 CPS with 25 games and wonder if that is too high or okay as is.

Well, if it's a per player calculation then lower numbers will be fine.  I was thinking it was global, and low numbers could create an issue I was thinking on, but not going to put any ideas out there

another question on this line...
if cps is too low... would commands buffer up waiting to go through, and could this cause server lag at times?
The reason i ask is I've noticed b4 on a server it got laggy once in a while, but after game op upped the cps it smoothed out...

Actually if the cps is set at a low setting, it will seem like lag.  Especially below 10.  The player is sending more than the server will accept and finally the helper he is using will buffer out.  So basically it is lag.  The purpose for the cps is to only accept from the users the amount the server can handle and to not let 1 or 2 people on fast connections eat up all the resources.  If  you have a lot of players on, the resources are shared more equally between players.  However if you set it too low for the machine you have and the amount of players you have, then the players will complain about it being too slow and figure it is lag.
 

And as a final answer to this question, the cps setting is a global however it is not a per machine limit it is a node speed limit. so a player who has say 3 nodes under there control on a 10 cps system wont be reduced to a 3.3 cps limit on each node but will have all 10 cps per node.

also on the point of the lag, the server being set on too high a cps will also lag, from the scripts that take too much resources from the connection, which will lag the others that aren't taking up the resources, so you need to set a medium that lets both work with out too much interferance. I usually set my server at 30 to 100 cps, cause if I set it to unlimited, the real intense scripts will let the server bog down to all others except the person who is running the intensive script. In which case would give that player an advantage, cause he is using all the servers available resources. But if you want to even out the server to both the script users and non script users, try a setting between 6 to 12 cps, although you may get some complaints from the users who use real intensive scripts, this will round out the server so even the non script user will have some chance, especially if he knows how to make and use macros.

Hope this helps.

I agree will everything Vulcan said here with a minor setting difference.  I usually set my server to between 8 and 14.   This setting largely depends on the speed of the server and the type connection you have though.  If it is on a T3 connection with high bandwidth, and a very fast server, you can set it higher and not really give anyone an advantage.  However, if it is a crappy connection or a slow server, setting it too high is going to give the scripters with fast connections a hugh advantage on speed, and they will be eating up all your bandwidth.   Think of it as a 2 inch water line feeding a bunch of smaller 1/4 inch lines with valves controlling the water flow.  The valves that are wide open are going to get the most flow and get the most water, but if all the valves are half closed, all the lines get the same amount.   But then again, if the valves are barely cracked, then none of the lines are getting much water.  You just need to play with the setting until you think it is right for your server and connection.