I really just can't get over how bad this "you can't run unsigned apps" thing is for, well, everyone. It is a depressing thought that this might be the future of software.
There is actually something else going on here. I have never seen the 'this app is damaged' error and I think it is because Flash creates those 'Projectors' in some incompatible way. Unsigned binaries are really not an issue. People who know what they are doing can completely turn the check off, or you can leave it on simply 'command-click and choose open' once to add the app to the whitelist. I do this all the time.…
Superficially, that makes it seem like not an issue. But it's sort of like when Sony added the "no class action" waiver to their TOS. Yes, you could opt out, but it still removes virtually any possibility of a class action suit since very few people did opt out. Similarly, it is possible to run apps that aren't signed, but most users won't, and that means that it isn't viable, from a developer's perspective, to produce unsigned apps.
Now, it's true that you don't have to go through the App Store review process just to sign an app, but that doesn't mean that Apple can't revoke your key on a whim (or in error).
The cost is also an issue. $99/year is a steep commitment for what used to be a pretty big segment of the Mac developer ecosystem. The common counterargument to this is "Really, you're going to complain about $99 when while working on a $2500 laptop?" But this is nonsense. If you're unemployed, in school, or working a low paying job while developing on the side, your computer likely isn't a $2500 laptop. It's probably a low end Mac and/or a hand-me-down, and you will keep riding that machine until it breathes its last gasp. $99/year is about the cost of your whole computer.
Now, maybe Apple doesn't care about a slew of small, cheap/free apps with low hardware requirements, but their users sure as hell should.