I was thinking about this today after reading the Spanish expression, No hay que confundir la velocidad con el tocino, one must not confuse speed and bacon. In English, of course, we say that you can't compare apples and oranges, and this seems to be known in French and Spanish as well, although in French it tends more often to be apples and pears (des pommes et des poires), a pair also used in Spanish (you can't add pears and apples, no hay que sumar peras y manzanas). The Portuguese reject the comparison of oranges and bananas (laranjas com bananas).
I don't know how accurate it is (all of the above I can confirm), but the Wikipedia article on apples and oranges gives a list of expressions for other languages:
Some languages use completely different items, such as the Serbian Поредити бабе и жабе (comparing grandmothers and toads), or the Romanian baba şi mitraliera (the grandmother and the machine gun); vaca şi izmenele (the cow and the longjohns); or țiganul şi carioca (the gypsy and the marker), or the Welsh mor wahanol â mêl a menyn (as different as honey and butter), while some languages compare dissimilar properties of dissimilar items. For example, an equivalent Danish idiom, Hvad er højest, Rundetårn eller et tordenskrald? translates literally as What is highest, the Round Tower or a thunderclap?, referring to the size of the former and the sound of the latter. In Russian, the phrase сравнивать тёплое с мягким (to compare warm and soft) is used. In Argentina, a common question is ¿En qué se parecen el amor y el ojo del hacha? which translates into What do love and the eye of an axe have in common? and emphasizes dissimilarity between two subjects; in Colombia, a similar (though more rude) version is common: confundir la mierda con la pomada, literally, to confuse shit with salve. In Polish, the expression co ma piernik do wiatraka? is used, meaning What has (is) gingerbread to a windmill?. In Chinese, a phrase that has the similar meaning is 风马牛不相及 (fēng mǎ niú bù xiāng jí), literally meaning "horses and cattles won't mate with each other", and later used to describe things that are totally unrelated and incomparable.
[Mikhail says, on the Wikipedia Russian claim, "Nobody says that in Russia! The phrase used is - не надо сравнивать божий дар с яичницей - which means 'don't compare God's gift with fried eggs"'... :)"]
[hghandi says, "In Iran there are two phrases used.
آسمون ریسمون کردن
is literally "talking about sky and rope". They only rhyme together (ASEMOUN, RISMOUN) but one is sky the other is rope.
The other phrase is
چه ربطی گوز دارد با شقیقه؟
literally meaning "what is the relationship between fart and temple?" temple as a part of body that is."]
An 1864 text says you can't compare apples and herrings; in 1901 engineers were saying you couldn't compare apples and potatoes; a 1908 text denies you can compare apples with eggs; in 1915 the American Produce Review denied you could compare apples and pears. But it goes back earlier than that; John Ray in his 1670 proverb collection gives four examples of false comparisons: apples and oysters (which Shakespeare also uses in the Taming of the Shrew), four-pence and a groat, nine-pence and nothing, chalk and cheese (the last of which still is occasionally heard).
Everything I've seen suggests that 'apples and oranges', specifically, is an American thing -- after all, we have long had both in immense supply. [Tailz says, "Apples and oranges is used with equal frequency on the British side on the pond too." I think I intended to say that it was of American origin! I've come across British writers using the expression, so my claim was certainly not right, as written, as even I knew. But even the origin claim is speculative.]
I think, though, the general moral to be drawn is that nothing is comparable to apples.