Difference between 什么，什么呢，什么吗 and 什么了?
你要什么？

What do you want?

你要什么呢？

And, as for you, what do you want?  (might be used, for example, after saying what you yourself want and then asking into the other person's desires.)

你在做什么吗？

This looks ungrammatical to me.  Without the 吗 it would be: What are you doing?

你做什么了？

What are you doing now?

The differences between these sentences, however, lie in the verb and the presence of the final particle (呢 or 了) in these cases, or not.  There are no special combinations at work with 什么, except in the case of #3, which has a problem because 什么 already signals a question in this case.  你什么也不要吗？ might work (= You don't want anything?), but I am not a native speaker, so I can't say for sure if it would sound natural (请教).  Or, for another example: 你知道什么吗？ (= Do you know something?).