What should I group together?

C.M., do not try to do all that in one day. If you do, all you will remember is a blur of quick glances at the famous sights, as you check them off your "to do" list.

Slow down. You'll want to walk a bit, not just in the Latin Quarter. And you'll need to eat occasionally. What about museums other than the Louvre? Paris is famous for its art museums.

Just my opinion here, but I'd skip the Seine cruise. I've been on it twice, and neither was very satisfying, or romantic. The second time especially, there were hordes of other tourists crowding the rails, blocking everyone's views, and talking so loudly it was difficult to hear the recorded narration. Now, if you could spring for a private cruise, perhaps with dinner or at least wine, that might be different.

I would definitely not try to do your list in one day. With only 2 full days and an evening I would leave Versailles for another trip. Personally I would not skip the evening cruise on the Seine, I loved doing this when the monuments were lit up, it was wonderful. I might instead skip the Ho Ho bus and just use a good map, the metro or bus, and walk to see the sights you have on your list.

It'll be a full two days, but you can do it. I wouldn't try and do Versailles AND Paris with just two days. Here's one way you might mix it up. Weather and the specific neighborhood you're staying in may influence the order of things a bit...

Saturday evening:
Evening Cruise of the Seine (recommend Vedettes Pont Neuf)

Sunday
Notre Dame
Louvre (Just to see the Mona Lisa, Venus de Milo, Winged Victory of Samothrace, Venus de Milo only)
Garnier Opera House
Walk around the Latin Quarter (for dinner)

Monday
Hop on/off bus tour
Eiffel Tower
Arc de Triomphe
Luxembourg Gardens
Evening Cruise of the Seine (yes, I put this in here twice, because it's an inexpensive and delightful way to wrap up your time in Paris. Just make sure you go on Vedettes Pont Neuf and sit on the top!)

I would group things geographically:
Evening 1:
Dinner in the 7eme or across the seine, in the 16eme, and then visit Eiffel at night time (fewer crowds!)
Day 1:
-perhaps start your day with jardin de luxembourg. this is proximal to many of your other stated interests and you can perhaps bring your breakfast and explore. make your way north from here to see st sulpice, then you'll hit blvd st germain.
-explore latin quarter. walk along blvd st. germain as you please; then make your way north up to st. michel. walk along seine and cross into ile de la cite. wait in line for notre dame.
Notre Dame
rest
evening cruise

Day 2:
utilize the hop on hop off to reach your geographically disparate locations, although the metro is very good in paris. Try to begin at the Louvre so that you'll waste the least time with the terrible lines there... from there, you can make your way through the tuileries and up the champs to the arc de triomphe. Personally I would avoid this part of the trip but if you have a high tolerance for times-square or disney-esque crowds then it will be fine. Possibly make a stop in the orangerie while on your way through the tuileries to see monet's waterlilies.
after the arc, go back on your bus and you'll eventually hit the garnier opera house. it's on the right bank, as is the arc. there is high end shopping around there. Depending on where you're staying, maybe take some rest at this point, and then depart for the evening cruise of the seine.

Hope this helps!!!

Thanks everyone.

Just my suggestion: I don't recall where those three items are located in the Louvre, but ... for time/money/all the walking involved, I'd highly recommend leaving the Louvre for your next visit and take in one of the house museums in Paris. The Musée Jacquemart-André is a delightful turn-of-the century townhouse donated to France by a husband and wife who were art collectors. I'd go back there just to walk up the staircase! One of Elizabeth Vigee-Le Brun's paintings is there and seeing it in person was a highlight for me. It is an intimate setting chocked full of antiques and art/sculptures (15-18th century). Also, it is virtually in the middle en route from the Opera House to the Arc de Triumph on your list. http://www.musee-jacquemart-andre.com/
The Musée Nissim de Camondo is another superb option, an 8 minute walk from the Jacquemart-Andre with the Parc Monceau in its backyard. Two Vigee-Le Brun's there:) So still in the vicinity of the Arc de Triumph and the Opera House. http://www.lesartsdecoratifs.fr/en/museums/musee-nissim-de-camondo/