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hankronTechnically speaking, any of the recent 1-of-1 insert sets would be the rarest, both because there can only possibly be one set and because few of the sets have been completed by a single collector.
On the other hand, it might be said that a 2002 1-of-1 card isn't rare when there are 20,000 different 1998-2004 1-of-1 cards, and another 7,000 to be produced next year. Unique and one-of-a-kind not being the same thing.
An example of a rare vintage set is the 1923 Maple Crispette. While most of the cards are scarce but available, there is (as far as I know) only one known Casey Stengle, transplating to one (as far as I know) possible complete set (as far as I know and so I've been told and the fact of the matter is that's the bottom line. If you know what I mean).