peroxisome. This year it's the turn of the nucleus. Yes, the nucleus itself.
Viral Eukaryogenesis: Was the Ancestor of the Nucleus a Complex DNA Virus?
This paper, from 2001, has been cited 60 times since then (thank you Web of Science), so it has attracted some attention but not a huge amount. Looking at the titles of some of the citing papers it is clear that this whole question is now wrapped up in the question of viral origins and our friend the mimivirus again.