My favorite tools are a propane torch or glass cleaner, depending on the environment.
For years, I used a Salt Gun, but my wife complained about the salt, and then one day the kids left it out in the rain and it stopped working. Since then, I have used these two tools. Each of them is far more effective than a swatter, even more effective than the salt gun.
With the torch, I give a quick press of the electric ignition to let out a quick burst of flame. You want to aim for just beyond the visible flame, and you will do fine. Depending on your aim, you will vaporize their wings, and perhaps even their appendages, and they will drop to the ground. Most of the time, I find tha they are instantly killed. You do need to be careful of your backstop or what ever the fly is perched on. You won't want to hit them if they are sitting on something fragile or flammable, but ceilings, walls, tables, counters, etc are all fine, as long as you are careful about the intensity and duration of the flame. Just give the button a quick flick, nothing more. I prefer this solution to the salt gun, and have scored may double and even quite a few triple kills with this, as you can angle the flame to wash over one or more flies if they are close enough. It also is possible to take them down on the wing, just be careful of where you aim it. It also does not disturb the nearby flies, so you can just move about a room taking them all down with a quick depression of a button.
The glass cleaner is useful for cases where the backstop would make the torch unsuitable, such as flies landing on a TV or monitor. Just give them a spritz, and they will be unable to fly and fall to the ground. While they may not be killed by this technique, I don't think that is necessary, as I police the body with the same paper towel that I use to wipe the cleaner off of the screen. If you need to have a lethal spray solution, and you want to leave dead flies laying around your house, you can pour some alcohol in a spray bottle. The spray bottle is also a tool that will allow you to reliably take down flies in the air.