Do you have to go thru Museum security lines before you even get to the ticket lines? Or, do you go thru the ticket line first, and then the security line?
Most museums. Security first: Louvre, Orsay, Orangerie, Pompidou, etc. But tickets first: Branly.
If you have a Museum Pass or ticket you can use a different and shorter security line at the Louvre (separate line at the Pyramid and bypass line at the Carousel), the Orsay (different door for ticket and pass holders), the Orangerie (separate line for ticket/pass holders). The Pompidou also has bypass as do most museums. Two places where the ticket won't do you any good with security, the Notre Dame Tower (only 20 are let up at a time and no one skips this line) and usually Ste. Chapelle where everyone usually, but not always, is in the same security line.
The Louvre is surprisingly not big deal with lines. The last time we visited it took us about 10 minutes for security at the Carousel and then we just got tickets from machines with no lines there at all. The Orsay on the other hand reliably has terrible lines for people without tickets; however you can buy tickets from the newsstand out front and use the designated security door which we did this fall.
What about the Eiffel Tower? I would assume that the ticket line is first, and then the security line?
There is security to even approach the tower, it is completely gated off now; once in you line up for tickets and security occurs as you approach the elevator and they take the ticket; if you have a ticket ahead then you just go to the leg designated for reservations and show the ticket and security occurs as you enter the leg for the elevator.
When I went to the Louvre in late September, there was a note for the Museum Pass that you could no longer use the Carousel entrance, you have to use the main entrance by the pyramid. I don't know if that's changed back?
I didn't go up the Eiffel Tower. We walked around it, just outside the fence.
We were at the Louvre in October and there was a bypass line to the right of the main line at the Carousel. We didn't have pass or tickets and it still only took us about 10 minutes to get through security there. The Louvre used to admit pass holder through the Richelieu entrance but they don't seem to do that now. They change such policies often and rather randomly.
And note, you can always use the Carousel entrance pass or no as no one has to show a ticket or pass for security. And if the Pyramid security line for pass holders is long, it might be quicker. The entrance to the Louvre is also the entrance for the bookstore, gifts shops along the way, food, cafeteria and other food services, so it is quite possible to go through security without even intending to visit the museum itself. Tickets are checked at the entrance to each wing and you can exit and re-enter all day.