Yes! Get the museum pass (passe de musee?).....available at the ticket counters in the major subway stations. This will bypass almost all lines and you won't be shelling out money over and over again. It made me feel better about doing a "quick run through" some museums....
Notre Dame......climb the bell tower. So cool!
"Behind" Notre Dame at the tip of the Ile de la Cite (that's the island Notre Dame is on) is a Holocaust Memorial. This is a quick walk-through area and won't take much of your time, and is worth seeing. Each light inside is a French (?) Jew that was killed in the Holocaust.
Near Notre Dame (still on the Ile de la Cite) is the Concergiere (the old prison) which again, if you take 30 minutes you can tour (using your museum pass). This is where Marie Antoinette was held. Check out the very big, very old clock on the outside of the building (riverside if I remember right). Right next to this is St. Chapelle, which as was stated before is EXTRAORDINARY!!!!!! There is a lower chapel where you will go "Hmmm, nice." and then the upper chapel....the stained glass windows will blow your mind. Seriously. It's the most beautiful church I've ever seen anywhere.
All the above are within a 4 minute walk of each other.
You'll spend a lot of time going up the Eiffel Tower. Even with moderate lines, plan on 2 hours minimum. But you kind of "have" to do it.
The Louvre, of course. Don't be overwhelmed. Check out the Mona LIsa and then just wander as long as you like. In the "basement" you can see the original castle walls of the palace of the Louvre, and a replica of how it was originally built (reminded me of Disney's Cinderella's castle).
The D'Orsay museum is much more manageable in size, and has much more recognizable art (VanGogh, Monet, Seurat...). You will recognize a lot there, and there is a lot of "pretty" paintings.
The Picasso Museum is short and sweet. You can traipse through it in 30-40 minutes and enjoy it immensely. The area around this museum is fun. Poke around.
The Pompidou Center is the modern art museum. There are incredible masterpieces and lots of CRAZY stuff....I mean laugh-out-loud crazy. Panty-hose filled with sand hanging from the ceiling. Alligator heads lit up with christmas lights. You name it and someone called it art. We enjoyed it immensely, even though we know nothing about modern art. The area around here is lively (younger crowd) in the evenings. We spent an evening here, which was great fun, poking around and trying hard not to split our sides laughing. Guess we're just country folk!
If your weather is good, the many gardens will be magical. Just check closing times as some are gated and close around 6 (?) in the "winter".
Take a boat ride. Maybe in the evening to see the lights?! It's hokey, but fun. Try to find a warm, dry night so you can sit outside. If it's raining, you can sit inside but then you can't see so well. Many take off at the waterfront near the Eiffel Tower.
When near the Eiffel Tower, wander over to the Rue Cler market area, best in the mornings for a very French scene of fruit and fish markets in the streets, bakeries and cheese and chocolate shops. Just a quick walk will make you feel like you're in Paris!