They can be used interchangeably, they are both ways to answer a question that you are unsure of the answer or you are indecisive. The difference, for me, is I would use 'I think so' as answer for a question I am not fully certain of the answer and 'I guess so' for an answer for something I am indecisive over. A: So have you made up your mind, do you want to got to the party? B: I guess so. A: So do you know where the party is at, is it at Johns house? B: I think so. You can also use both as a passive agreement. ('I guess so' is more passive) A: Wow, so Tommy really did turn out to be a jerk, didn't he? B: I guess so/I think so I hope this helps!