Indeed the situation is a bit complicated and not totally well understood. Archaea and bacteria are superficially very similar, they're both small, have circular chromosomes, and not a lot of internal complexity. However, there are some very important differences, most notably they have very different cell membranes.
The origin of the eukaryotic cell is a very difficult subject, as it evolved over 2 billion years ago in organisms that don't fossilize well and there are no living descendants of intermediate forms. (E.g. every known Eukaryote is descended from a eukaryote that already had mitochondria.) My understanding is that the leading theory is that the eukaryotic cell was formed by endosymbiosis between an archaeon and two bacteria. In that model the nucleus is descended from a methanogenic archaeon, the cell membrane is descended from a myxobacteria, and the mitochondria is descended from a proteobacteria. But this is not fully understood, and there are several competing theories on the details.
One place to start reading about this (beyond wikipedia) is a nice article by Carl Zimmer in Science.