Wii Transfer music and picture sharing will only show the first 1000 photos per iPhoto album. If you have more than 1000 photos in a single album, you may want to create new albums in iPhoto to separate out the photos into sets. You will need to restart Wii Transfer for it to notice any changes made in iPhoto.
This limitation is imposed by Wii Transfer because larger sets of data can crash the Nintendo Wii, which has less memory than a traditional computer. If the Wii does crash, you can restart it by holding down the power button for several seconds until it turns off.