I am just learning how to implement the Nested Set Model but still have confusion with a certain aspect of it involving items that may be part of multiple categories. Given
Old thread, but I found a better answer to this problem.
Since apple can have different color, your structure is a graph,not a tree. The nested set model is not the right structure for that.
Since you mention in a comment that you're using Mysql, a better solution is to use the Open Query Graph engine (http://openquery.com/graph/doc) which is a mysql plugin that lets you create a special table where you put the relationships, basically parentId and childId. The magic is that you query this table with a special column latch depending of the value passed in the query will tell the OQGRAPH engine which command to execute. See the docs for details.