The question of options is certainly a complicating one. Since it will undoubtedly have a strong effect on the Cubs' personnel decisions this month, let's take a quick look at what that effect might be.
In baseball, the options system prevents teams from stockpiling talent in their minor league systems. Each player has a limited number of "option" years; when those run out, that player must either be permanently included on the major league roster, or he's made available to the rest of the league.
Three Cubs pitchers vying for the two remaining bullpen spots are out of options: Angel Guzman, Chad Gaudin, and Jason Waddell. If Lou doesn't carry these guys on the 25-man roster, they'll be fair game for every other team in MLB.
Options aside, I think Hart and Waddell are the best choices for the 11th and 12th spots on the pitching staff. However, I could very easily see a scenario where the Cubs decide to keep Gaudin on staff while Hart hones his craft in the minors during another option year, and avoiding the options problem.
As a final note, the options issue essentially makes Samardzija-to-Triple A a no-brainer, since Jeff does have options remaining at this point.