As mentioned above, I'd recommend the Paris Museum Pass. This is different than the Paris Pass (which costs like 3 times as much and doesn't really provide much more benefit). It gets you into most of the main sites, like the Louvre, D'Orsay museum, Versailles, Saint Chapelle, Arc de Triomphe, etc for no extra cost. It's worth the money unless you're only planning to do 1 or 2 of those. In some places you can skip lines with the pass. Sometimes you still have to go through a security line but get to skip the ticket line with the pass. It doesn't include the Eiffel Tower, and you should get tickets well in advance if you want to go up.
Regarding other places with long lines:
- Paris Catacombs - You will wait for hours if you don't purchase tickets in advance.
- Versailles - Go at least a half hour before it opens or you will wait for many hours to get in. The only way to skip the line is to buy a timed ticket. But since the untimed ticket is free if you have the Paris Museum Pass, just go really early. (by the way, Versailles is just a short bus ride from the Paris Temple if you want to see that)