Hmmm.. For me there's not really a big difference in the meaning. If anything, then it would have to do with the feeling of the sentence. The first one has a comma in between, so that gives a sense of rest. The second one doesn't stop so it runs smooth. By the way, the second one is supposed to be, "the apple (in->is) on a plate" like the first one. I assume this was just your typing mistake! More simply, you would say, "The apple is on a clean plate". Hope that helped! :)

First point - don't forget to use capital letters at the start of each sentence. This is not an optional feature of English. Nobody will take your writing seriously if you make such a basic mistake as starting a sentence with a lower case letter. If your English is advanced enough for you to be worrying about the subtleties of comma use, you should really be able to use capital letters appropriately. Secondly, yes, there is a difference between the two. The sentence which you want to say is this: The apple is on a plate which is very clean. In this sentence, the clause 'which is very clean' refers to the plate. If you insert a comma, this changes the meaning of the sentence. The addition of the comma makes the word 'which' refer to the statement 'The apply is on the plate'. It means that the fact (that the apple is on the plate) is clean. A fact can't be clean. This doesn't mean anything. You could say, possibly: The apple is on a plate, which is surprising. The apple is on a plate, which is useful. These sentences mean that you think it is useful or surprising that the apple is on a plate. But 'The apple in on a plate, which is very clean.' ? No - it makes no sense.

2 is wrong