ShadowWulfe: Even if I was a Rebel (who in Geneforge 3 are kind of d-bags), from a magic user's perspective, why would you want to go bonkers?
I believe that the main attractions are that it allows shapers/lifecrafters to learn new skills without having to spend years as an apprentice, pay large sums of money to an experienced shaper for training. The fact that cannisters seem to have a supernatural allure to them for those with shaping skills (just look at Greta's reaction when she first sees one), are increadibly addictive, and alter the user's mentality to the point where they no longer see any downside to using them is just icing on the cake. Since they also cause physical mutations, you can bet that any shaper who starts showing signs is going to be in ostracised at best means that once you start using them it becomes near impossible to stop.
Many creations and rebels (particulalry lifecrafters) will not respect rebel shapers that refuse self-shaping. Some will respect you more if you shape yourself because it is seen as becoming like a creation, and as a symbolic way of burning your bridges behind you.
Mostly though it is about the power, cannisters and geneforges allow any ordinary outsider to rapidly gain power that would take a shaper years if not decades to achieve through careful study, and means that they don't have to abide by shaper rules or restrictions. Basically, cannisters are a free ticket to near infinite power-a cannsiter character will always be more powerful than a cannsiter free character in a given geneforge game by the end.
AS for how it affects geneforge 3...most of the effects will be noticed within the game, rather than the ending. The difference between the cannister and no cannsiter rebel endings is microscopic, and the difference between the cannister and no cannsiter shaper endings is only slightly more noticable. Still, there is a difference, and while it might not be terribly noticable in the ending, your cannister addiction status will pop up from time to time in game, which is more than can be said for geneforge 1 and 5 (no effect whatsoever). Geneforge 4 is the game where cannsiters have the most effect on the story and ending (ironic, since the character is a rebel)
Personally, I have never played a cannister addict sicne the first time I tried it-in Geneforge 3. Even though the effects of using them are not huge in most of the games, I definately had the feeling that I was compromising not only my character's morality and mind, but their status as a human being. One of the main reasons I never play as a rebel is because of the inseperability of cannisters and the rebel movements. I would reconmend not using them, I personally get a great deal of satisfaction beating the geneforge games (even 5, where it had absolutely zero effect on anything), knowing that I didn't compromise my integrity in the journey there.