The best flight sim depends largely on which eras and style of flight most interest you. Here are my favorites for the major genres:
WWI: Red Baron 3D
This is practically a winner by default, RB3D (and RB-II, the game it was based on) is the only WWI flight sim released in the last five years. When this game came out it stunk on ice. But in the years since Sierra patched the major problems and the user community has created some great mods.
WWII (Light): Jane's WWII Fighers and Microsoft Combat Flight Simulator II-Pacific Theater
A light sim is one that places more emphasis on action than flight model realism and historical detail. Still, these two are hardly arcade games. Both are great fun to fly, have terrific graphics, and are very immersive.
WWII (Deep): IL-2 Sturmovik and Battle of Britain
Others have sung the praises of IL-2, and they're right. The online play of IL-2 is to flight sims what Ultima Online was for RPG's, it truely redefines what is possible. BoB is a hidden gem, and maybe a better game if you prefer offline play. The flight models and graphics are very good, but the great thing about this game is that it runs in real time. The actual Battle of Britain lasted just 28 days and the game only gives you that much time to either save or lose the battle. And because the forces were so numercially mismatched, its not hard to believe that the outcome could truely turn on your performance. Great stuff.
Modern Military Jet (Light): Jane's USAF
The flight and weapons modeling almost defies crediblity, but USAF is still a lot of fun. It is like Need For Speed with wings. A couple of unique features make it shine. First, it covers Vietnam with the F-105 Thud and F-4 Phantom, and you can fly actual missions from that war. The other thing I like is how it incorporates all types of tactical flight on a mission. You have to assign several squadrons of different types of planes to complete a mission and jump between them. In emphasising the duties of each fighter type to completing a mission, USAF is actually more accurate than any other sim on the market.
Modern Military Jet (Deep): Flanker 2.5
You'll have to hit eBay to find this one but its worth the effort. This is the best flight and weapons model I've found in any flight sim, with gorgeous graphics and an immersive campaign. Oh, and you don't need to download an effing huge patch file to make it work. (If you're on a dialup, don't even think about buying Falcon 4.)
Helicopter: Jane's Longbow Anthology
This is a tough call. The Enemy Engaged series is newer, is just as accurate and has far better graphics. But comes up far short on documentation. It can take weeks of dedicated work to figure out how everything works. Commanche 4 is a better choice for a casual sim player, but the hardware requirements are as serious as a heart attack. Its largely a victory by default, but the Longbow series remains the best helicopter sim I've ever played.
Civilian: X-Plane 6.xx
Unless you are a real or aspiring pilot looking for a sim to keep your pattern procedures sharp, there is no reason to pick Flight Simulator over X-Plane. X-Plane lacks the last-button detail of FS2002, but the flight model is much better and what it trades in cockpit detail makes it easier to fly and have fun. The user community for X-Plane is outstanding, too.
BHD