Lock-On's the best free modern flight sim I've ever played.
I think that for the hardcore sims category, Falcon 4 Allied Force is the best sim available now (but probably I don't consider Lock On the best because... err... I got low FPS with it, and I never tried it with the new graphic card
The Strike Fighters/Wings over Vietnam/Wings over Europe/Wings over Israel series is also quite good, but it's far less complex compared to F4 and LOMAC ("less complex" does not mean "Ace Combat like", it means that flight dynamic and weapons loadout are correct, simply it doesn't simulate each cockpit button like F4 and LOMAC, and thus is preferable for newbies).
For WW2, the best is without any doubt Il-2 1946, especially after I discovered the mod which makes almost all airplanes flyable. Also the old Fighter Squadron - Screamin' Demons Over Europe is quite good, I discovered it after hip63 posted here a link to his FS-SDOE forum.
For WW1... well... the last one I played was Red Baron 2
For civilian flight, I think X-Plane is superior to Flight Simulator (I haven't tried X-Plane 9 yet, but I will do that soon), especially because, since I'm studying aerospace engineering, I like the idea of an airplane editor included in the package