The November/December 2011 issue of IEEE Software has a good article by the Climate Code Foundation's Nick Barnes and David Jones titled "Clear Climate Code: Rewriting Legacy Science Software for Clarity". In it, they describe how and why they rewrote a program used to calculate and compare global surface temperatures based on historical data. The original had been attacked by climate change denialists, first because it wasn't publicly available, and then because it was tangled and hard to run. Their rewrite produced something smaller, faster, and much easier to understand; most importantly, though, it validated the results of the initial program.
Which made me wonder: what scientific program would you most like to see rewritten? To keep the question realistic, it has to be something small enough that two good programmers could do it in six months or less. What would you like rebuilt, and what do you think the benefit would be?