The Twins need to set their 40 player roster by Friday in preparation for the winter meetings and the Rule 5 draft. I did an evaluation of players who are eligible for the rule 5 draft here:
Since then, I have learned that neither Tosoni nor Slama are eligible since they were draft and follows and, as noted, Ramos is already on the roster.
The Twins currently have 35 players on the roster, so they have five openings. Here are the players I think they should protect:
Guerra, Burnett, Waldrop, Van Mil, Singleton
I think these five players have the most upside as major league players. I may be over-valuing Singleton if his defense isn't up to snuff, but the reports I have seen say he is a solid defensive player with enough range to at least play second base in the big leagues. His bat looks like it will be major league as well.
To be clear, I don't think these are the players the Twins will protect. My guess is that Valencia will be protected. The Twins seem to be high on him despite his struggles at AAA last year. Delaney is another possibility. Both of them are closer to the big leagues than any of the players on my list. There may also be some surprises from the lower minor leagues, but usually those guys don't stick even if they are taken in the Rule 5 draft. Of course, there are exceptions like Johan Santana and Roberto Clemente. You don't want to the GM who lets a future Hall-of-Famer get away.
The other thing to remember is that the Twins can still open up roster spots by releasing players after they have set their roster. That is what happened with David Ortiz. They released him to open a spot prior to the Rule 5 draft after not being able to find anyone willing to trade for him. They can wait until they see who is available in the Rule 5 draft to decide if there is someone they like better than their own guys who are on the roster.