SIMULATOR COMPONENTS
So what exactly will it take to provide your body with these all-important sensations of flight? It might not be as complicated as you think. There are three categories that we will be dealing within this subject - sight, motion, and sound. 1. VISUAL CUES
First of all, it helps if the inside or your cockpit resembles an aircraft. If you get in the cockpit and it looks like the cab of a truck, well, that just kind of ruins the experience. A steering wheel and gear shifter is definitely out of the question. The outside of the cockpit is a little less important, but a realistic looking outside shell can be a nice touch. However, the most important visual cue that will help you feel like you are flying in a real plane is your looking out of the aircraft view. Try watching an airplane video on a small screen TV, then go to an IMAX theater and watch a film showing the blue Angles flying. If you've seen a film like this at an IMAX then you know the point that I am trying to make. Because all of your peripheral vision is seeing the huge IMAX screen your body begins to feel like you are really doing loops in the air even though your brain knows that you are just sitting in a chair on the ground watching a large video picture. This principle also applies to your simulator, the more that the outside view fills your vision then the more you will feel like you are really flying. If the view is big enough it can be a very powerful cue to your body even without motion and sound cues. Also, objects in the simulation will seem more lifelike because they are large. Flying by an aircraft carrier is very impressive when you are using a six-foot wide projection screen. Of course the problem with a large display system is its higher cost, but if it is in your financial reach then in my opinion you should go for it. If you're still not convinced then go watch a good aviation video or movie on a large screen, then play your favorite simulation on the 15-inch computer monitor. See which experience makes you feel more like you are flying..
Some people opt for a second option, a Fresnel lens with a large monitor. The biggest pay off when using a Fresnel lens is that it gives you a great sense of depth perception which helps you to feel like you are really at higher altitudes and looking at objects a distances far away. If you have to use a smaller visual system for the outside view because of cost or the lack of room, then a quality Fresnel lens is without a doubt the way to go.

2. MOTION CUES
There are multiple motion cues that you can use independently or together to give your body the sense that your cockpit is really in motion. 

SONIC TRANSDUCERS
The best way to get a great sense of motion with little cost is to use sonic transducers. These little gems turn sounds into vibrations rather than into a lot of loud noise. Transducers placed in the bottom and back of your ejection seat are great for letting you know that you are in afterburner or that you have just landed. My thought on this is to use two large transducers and one small one in your seat with one large transducer placed behind your back and the other large transducer placed beside the small transducer under your butt. When you are flying, the large transducer against your back and the small one under your butt will activate from the sound of the afterburner. You will get the feeling that a large engine behind you is pushing you forward because most of the vibrations are coming from the large transducer behind you. At the same time, the smaller one under you gives you just enough vibration to let you know that you're in motion without taking away from that sense of acceleration in your back. When you put your landing gear lever in the down position it should be rigged to move a switch that cuts off the transducer behind you and turns on the large transducer under you. When you land the seat will rumble under you causing it to feel like you really touched down. Placing a transducer between your feet on the floor of the cockpit is great way for rumbling the rest of your cockpit and in particular, your rudder pedals. This way you will feel your plane though your rudder pedals, and anything else you touch.
Of course when you take off you will use afterburner, but the system I just described turns off the transducer behind you. To get around this run wiring to your flaps handle. The settings for the flaps on take off and landing should be different, so when you have the flaps handle in the take off position it should be attached to a switch that opens your transducer circuit to the big transducer behind you. Now you have afterburner vibrations on takeoff. However, if this platform is used with landing on aircraft carriers or when doing touch and goes you might want to also have a flap setting that leaves the rear afterburner transducer on. I have used a computer subwoofer system with my sim but it became obvious that my friend's sim with transducers was much better because it helped keep the over all volume down while at the same time providing a much better rumble. Be sure to route the wiring going to the transducers from your sound card through an amplifier and equalizer that can turn up the base sound and cut out all the highs. You can also use FMODs to cut out the highs coming from your sound card to your Transducer. Transducers are what I would use if I were not going to use the VRF feedback seat. It is a motorized seat pad that gives those subtle motion cues that a transducer will not give. With the simulations it supports, such MS Flight Simulator, it actually reads data from the sim to control the vibrations. This is really great for helping you feel like your cockpit is "rolling" or "pitching". You can read more about it at http://www.vrf.com/default.htm. A force feedback joystick works well in conjunction with transducers and the VRF seat, especially with aircraft that have to be trimmed manually. 

G-SUITS
G-suits probably provide the best cue to let you know that you are pulling g's. While they don't provide you with that feeling of being smashed, g-suits do provide a cue that keeps you physically aware of the fact that you are in a hard turn. If you know that suit is going to give you a hard squeeze, you might put a little more thought into that turn before mindlessly pulling back on that stick. In real fighters the suit typically kicks in at about one and a half g and continues to squeeze harder as the g's build up. The only system in home built cockpits to control g-suits, that I currently know of,  are mechanical links to the joystick. When the joystick is pulled most of the way back, a valve opens to inflate the g-suit. When the landing gear is in the down position the g-suit system is overridden so that you don't get an undeserved squeeze when on the ground. A small 12V DC air compressor works well for supplying the air. 
The preferable system would be to have data from your simulation running the g-suit. The story by Erwin Neyt told how feeling the effect of g forces actually cued him to the attitude of his T-37, and a g-suit driven by simulation data could have the same effect when the simulation blanks out the monitor to simulate vision black out. I don't know of any home builders successfully finishing that kind of g-suit system yet, although I bet some might be close. Like everything else, it is only a matter of time before it is developed.

Actual Motion
The other big motion cue is to have your cockpit on a motion-based platform that moves the whole cockpit. There are three ways to set up your motion system that I am going to cover. The first two are for cockpits where the simulation does not have an open source code and the motion must be initiated by using an alternative input system.

Motion System A
The first system uses a mechanical link directly to your joystick for control of the platform and in my opinion this fits in the "wow, that was a great game" category. It is by far the cheapest motion platform and in this case I think you really do get what you pay for. The platform always moves with the direction the stick is moving and the cues sent to your body are wrong a large part of the time. In a real plane if you turn to the right you shouldn't feel yourself falling to the right as long as you are in a properly balanced turn. If anything, you should feel like something is trying to shove you through the floor of the aircraft. In reality, your body really IS being shoved into the floor of the plane because the aircraft is forcing your body to change direction.
When you pull back on the joystick, you shouldn't feel yourself being pressed into the back of the seat unless you are going vertical, instead you will once again be forced onto the floor by g forces. Personally, when I have flown in motion sims that has motion systems providing unrealistic motion cues it takes away rather than adds to the experience because I can sense that it is wrong. I once was sitting in a ride where the seats moved in relation to a big screen to make you feel like you were turning upside down doing rolls and boy did it work! I then went next door to a P-51 sim that really did turn upside down, but the cues were all wrong and the ride was boring because it felt so fake. The owner of the system bragged that nobody had ever become sick in his simulation. That is because the motion platform of the simulation moved directly in sync with the visual picture. That is not what real flight is like. In real life what you see and what your body feels can seem contradictory and then Tada! You have air sickness! So in my opinion, lots of bad motion cues are worse than no motion cues at all.

Motion System B
The second system still uses a mechanical link for control rather than data from the simulation software, but it also utilizes input from the throttle(s), speed break, and toe breaks. The actual movement of the motion base is accomplished through the use of a hydraulic or pneumatic system. Mechanical links to the joystick and throttle activate electrical circuits that in turn control the movement of the platform. If you slowly turn your joystick to the right the platform doesn't move at all and you feel nothing. But If you yank the joystick to the right then the platform rapidly leans to the right and causes you to momentarily twist to the left, just like the category A. system would do. However, the platform will then move back to a centered position and the cockpit will feel balance so long as you do not rapidly move the joystick again. The purpose of this motion system's roll axis is not to make you feel like you are leaning to the right. Rather, it is to give you that feeling of being tossed about when your fighter suddenly rolls rapidly. 
The platform's pitch axis is controlled by the throttle, the speed brake, and toe brakes. When the throttle is placed in afterburner that will cause the simulator to tip back. This causes your body to be shoved into the back of your ejection seat and gives you a great sense of acceleration. If you have your toe brakes engaged, it will override the motion platform and it will not tilt back because you are on the ground and should not be accelerating, at least not beyond leaving tire rubber on the ground. If you hit the toe brakes the platform will momentarily tilt forward to give you the feeling that you are de-accelerating. If your flaps are up and you hit the speed brake switch the platform will momentarily tilt forward. With flaps down you won't feel the effects of the speed brake because you are moving to slow.