There are at least two options that can plausibly be called the least important of the powers that are given to Congress by Article I of the Constitution.
First, there is the power that is given to each house of Congress to judge the results of its own elections. In other words, if there is a disputed election to the House of Representatives, that body gets to decide who actually won the election. Today, this is a very unimportant power. For the most part, the process of elections is carried out by the states and Congress plays little role in it. For example, the Senate had nothing to do with the recount in the Minnesota senatorial election of 2008. That election was decided by state elections officials and the state supreme court, not the Senate.
Second, there is the power to grant letters of marque and reprisal. This one was an important power in the time when the Constitution was written. Today, however, the idea that Congress would ever use this power is very hard to credit. We no longer live in an age where private citizens would go out in ships from the United States to attack the shipping of a foreign country. Therefore, this is a power that is surely completely unimportant.