Best times in Paris

The Musee d'Orsay is open late on Thursday and the Louvre is open late on Friday so you could do evening visits to both, the lines are always less in the evening. If you're not getting timed entry tickets ahead of time the ET is best done when it opens in the morning, go about an hour or earlier before opening - grab a croissant and coffee and have breakfast in line. Also, if you're fit enough to do stairs, then climb to the 2nd level and take the elevator from there (separate ticket) to the top. Lines are always much much shorter to climb the stairs.

I went up the Eiffel Tower at 10:30 am on a Tuesday and it was great--not crowded on any of the 3 levels, could move easily and take photos, no line for the toilet, etc. The D'Orsay was my favourite museum, arrived right about opening time on a Wednesday and by the time I left a couple hours later it was noticeably more crowded, though going in the evening might be great for you; it was for me at the Louvre, I knew an hour would do me perfectly there and entered through the lower Carrousel du Louvre shopping center entrance, no lines at all, pass or not. Just a couple of people ahead of me for security check.

Get there 1/2 hour before they open. I wish I could motivate my wife to get up early to go see attractions. Always shorter lines and cooler temperatures. Pass or no pass I'd still get tickets ahead of time because ticket lines are usually longer than security/entrance lines.

Richard makes a good point -- you don't have to buy the Museum Pass to have tickets in advance. You can buy tickets for the museums separately ahead of time without buying the whole Pass.

If you go in the evening - to any museum or attraction - make sure to check the official website to find out when the box office closes and the last tickets are sold.
Depending on the museum or attraction, the guards start shooing people out about 30 - 45 minutes before the "official closing time". If you go too late, you won't see much.

Thanks for all your suggestions. So just to understand if I buy the individual tickets in advance I will skip the ticket lines but still wait for in line for entrance. Somebody mentioned timed tickets . What exactly is that all about?

I would not go to the Orsay without a ticket in hand since you have so very little time to waste. When you have a ticket in advance you go into a different door for security and thus skip the long long security line out front. It is less an issue with the Louvre since there are several entrances for security, but with a ticket ahead you can use a bypass line at the pyramid for security. Tickets at the Louvre are not checked until you are entering a wing of the museum, the longlines are for security. Once inside you can use ticket machines for tickets and the lines are short for those generally. The Carrousel entrance from the mall under the Louvre has usually when we have gone had a fairly short security line which moves quickly compared to the long lines at the Pyramid. More people know about these days so it isn't quite as short as it used to be.