Question: I've heard people sarcastically respond with sentences of the form "then [effect of persons actions]" even though the person was not soliciting for advice. 

For example  

Joe: "I wrote my paper on why George Bush was a good prime minister for Canada"  

Jane: "Then you are going to get a bad mark"

Should it be "then" or "than"? Initially I thought "than" as it shows the relationship between writing a poor paper and receiving a poor mark, but since it's talking about something hypothetical that may happen in the future it would be "then".

Answer: 
"Then".

"Then" refers to the sequence of actions. "Than" refers to a comparison between two things. In your example, "you are going to get a bad mark" follows, and is the effect of, "I wrote my paper on why George Bush was a good minister for Canada". 

Since the second action results from the first, we are dealing with time order, and "Then" is appropriate.
In this case, you are looking for "Then" because "then" is a transition word that helps communicate a sequence of events. In this particular example though, I might suggest the word "consequently" or even the phrase "in that case," as they may be more clear.