Both are great games, but I'd give the nod to SMB3. It took a far bigger leap in quality from the previous titles than SMW did. SMB3 absolutely kills the first two entries, while SMW, as shown in this thread, isn't even considered a better game than SMB3 by some people. You'd be hard pressed to find people that would pick either the original SMB or SMB2 over SMB3.
That being said, Yoshi's Island is the title that I enjoyed the most. I know I'm definitely in the minority in regards to that though.







