The San Diego Padres' Paul DePodesta provides some interesting considerations: "These can be tricky decisions. On the one hand, you'd like to protect as many players as possible. However, on the other hand you have to anticipate roster moves that could happen between now and Opening Day in 2009. How many spots may we need for Major League free agents? How many players could we potentially outright or non-tender? Do we want to leave some spots open for potential waiver claims? Another part of the game is whether or not you think a certain player would, in fact, get selected in the draft AND if you think that player has the ability to stick in the Majors for the season. Sometimes teams will protect a lesser prospect simply because he has a greater chance of being taken or even because of organizational needs/depth going forward."
"When weighing the risk of a player getting taken, it can be counterintuitive. It would seem logical that the best way to protect a player would be to put him on the 40-man roster. That is often, but not always, the case. Sometimes, for players who are borderline roster considerations, you may be safer by leaving him OFF the 40-man. The reason is that if he's taken in the Rule V, he has to stay in the Majors or else be offered back. However, if for some reason (add a free agent, add someone through trade, need someone during the season due to injury) you need to add a player to the 40-man at a later date, you may be forced to outright someone to make room. When you outright a first year roster player, he still has all of his minor league options, so teams can claim him and send him right into their minor league system. In short, it's much easier to lose a player trying to remove him from the 40-man than it is to lose him via the Rule V draft."