Prokaryotes vs Eukaryotes

First off, I'm mildly surprised that your microbio prof assigned this question, since Prokaryote vs. Eukaryote is not a true dichotomy. The Eukaryotes are their own domain, but when one says Prokaryote one is merely saying that the cell has no nucleus which is true of two very different domains, the Bacteria and the Archaea. Those two domains are as different from each other as each is from the Eukaryotes.

My home internet is being crappy so I've not been able to find any good websites for you to look at, so my main suggestion is to go find a reference librarian at your college or public library to help you track down some good review articles. Your college would probably be better, as they're more likely to have electronic subscriptions to various journals, while a public library might be limited to big names like Nature, Science, PNAS, and Cell. Using Google Scholar, rather than vanilla-flavored Google, might also help you out.

As for the specific issues, I can help you out on some, but you'll need to find other sources since some schmuck on a message board with a Bachelor's isn't going to look terribly great in the Works Cited section of your paper.

Again, this is a poor question, as Archea and Bacteria do things differently and will involve different mechanisms to accomplish the same tasks. However, based on gross cellular archetecture, the two domains can be lumped together for the purposes of pointing out how odd the Eukaryotes are.

• The ER and Golgi are both used to package cells for inclusion in membranes and for excretion. Non-eukaryotes generally have only their cell membranes, with possibly a cell wall, and nothing internal, so they just don't internalize the synthesis of trans-membrane proteins and proteins marked for excretion.
  
• One of the big functions of the nucleus is to provide spatial, and thus temporal, separation between transcription and translation. Prokaryotic ribosomes usually start translation as soon as there's enough of an mRNA transcript to latch on to.
  
• Subscribers of the Endosymbiosis Hypothesis, which is more or less everyone nowadays, think that the Mitochondria are decended from bacteria very like modern purple sulfur bacteria that formed symbiotic relationships with the early eukaryotes. The early eukaryotes then internalized their symbiotes (endo- meaning, roughly, "inside" or "internal"). The Ox-Tox Hypothesis posits that the eukaryotes partnered with the purple sulfur bacteria in order to minimize the damage caused by the harmful Oxygen which was being pumped out bythe cyanobacteria.
  
• A subgroup of the early eukaryotes, the predecessors of the Plant kingdom, did the same thing to early cyanobacteria which resulted in chloroplasts.
  
• I can't help you much with lysosomes and peroxisomes. Lysosomes are areas "external" to the cell lumen which can safely house and store enzymes which degrade nearly everything else. If a non-eukaryote needs to degrade something, it generally just secretes whatever it wants done soon after the need for it arises. Peroxisomes harbor enzymes that rely on peroxides and radical chemistry to perform certain steps in various metabolic pathways. Theses are specialized structures, and off the top of my head I can't recall a direct correllate with non-eukaryotes, but some bug out there somewhere probably does soemthing similar.
  
• I recall reading an article about some lab group finding an archea that actually had an endosymbiote (something about an H+ gradient if I remember it rightly...). Find it and cite it toillustrate the point that the Prokaryote vs. Eukaryote divide is not a matter of black-and-white comparisons.

I hope this helps, or at least hasn't confused you too thoroughly.

some helpful websites i've tried were these two: biologybinder.com and cellsalive.com. :typing

hope this helps and good luck!