Therefore, its basically 'apples and oranges'.
Those are quite easy to compare. For a good example, see my sig.
Amusing link. The way i see it, the problem lies within the very definition of the word comparison.
1 : to describe as similar <compare an anthill to a town>
2 : to examine in order to discover likenesses or differences <compare two bicycles>
3 a : to be worthy of comparison <roller-skating does not compare with ice-skating> b : to appear in comparison to others <compares well with the rest of the class>
4 : to inflect or modify (an adjective or adverb) according to the degrees of comparison
http://www.wordcentral.com/cgi-bin/student?compare
In the analogy, it is clear that they're using the 1st definition of compare, saying that you can't compare apples to oranges because they're not, in fact, similar. But this is false, because you can, in fact, compare very different things, like the very example in the definition "compare an anthill to a town".
In addition, in most arguments, the definition used is the second one, "to examine in order to discover likeness and differences". Using the first argument to refute another argument that is using the second form of compare, is in fact committing a logical fallacy by reducing the actual meaning of the word compare in the context.
The fact is, you can compare anything to anything, both in the first and second meanings of the word Compare, but the adage attempts to extract a different meaning from the first definition, that is more restrictive than it actually is, i.e "to compare similar things". It's a fallacy, first and foremost, because you can't determine similarity before using the more broad form of compare, which is the second definition, and thus, the fallacy contradicts itself, since by stating that apples and oranges are different, means a form of comparison has already been made in order to produce that sentence.
So, not only saying "you're comparing apples and oranges" in order to reduce the value of a given comparison is a logical fallacy, it's also patently wrong.