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PaulSean, it depends what you mean by the most valuable set. I believe the two sets of cards that have sold for the most money were a Cracker Jack set and a 1952 Topps set. But those sold for so much money only because the cards were all in nearly perfect condition. If you took the PSA 8 T206 Honus Wagner card and added it to any T206 set, it would sell for more than even these very high grade Cracker Jack and 1952 Topps sets.
If you're looking for the most valuable set when you factor out condition, there are lots of candidates. An N172 Old Judge set would sell for a fortune in any condition if it existed. So would a set of N173 Old Judge cabinets. The T215 Pirate set being auctioned by Mastro at the National Convention will also sell for a fortune. An E107 caramel set would also sell for a fortune. Any of these would sell for dozens of times more money than a Cracker Jack set or 52 Topps set in similar condition.