From Homestar Runner Wiki
Flash is the program used by The Brothers Chaps to create the Homestar Runner cartoons and games. It is also the software used by The Cheat to create the Powered by The Cheat cartoons. These games and cartoons can then be played using the Flash Player included with most modern web browsers. Although the program has been renamed Adobe Flash, since Macromedia was bought out by Adobe, the version used by The Brothers Chaps is still attributed to Macromedia.
Though The Brothers Chaps generally use a PC to run Flash, The Cheat apparently runs the program on a Tangerine Dreams computer. It was also revealed at Flashforward 2006 (or rather, in the interview before Flashforward 2006) that TBC use Flash 5 to create their cartoons.
It was later stated in the Late Night JengaJam Interview that Mike would rather animate on a Mac, but "[they] use Flash 5, which is like six versions old, or something, and Flash 5 will only run in Classic. ... It doesn't run very stable at all. It crashes a lot and stuff. So if we could ever figure out a way to make Flash 5 run smoothly on a Mac, we would be more likely to just do more work on that." Matt immediately suggested to just run a Windows emulator under Mac OS X.
The Macromedia Flash program on The Cheat's computer was first seen in the Strong Bad Email "crazy cartoon." The program also made an appearance at the beginning of Labor Dabor, and on Main Page 22. However, each of these appearances was only a momentary glimpse of the "Timeline" area of the program. The "Mixer" toolbox appears in virus when the Sketchbook button is clicked. Flash's 10th Birthday is set entirely in the program itself, and was made to celebrate its tenth birthday.
 Flash Player
Most of the cartoons require version 6.0 of Flash to play, but some require version 7 (Stinkoman 20X6) and recommend 8. The FAQ recommends that you get the latest version of Flash, currently version 11.