You can recognize Intel only apps prior to trying to install them. I downloaded the new version of CronniX 3.0.1, which the developer accidently compiled as an Intel-only app, instead of a Universal Binary. After I had mounted the disk image, I saw a white "not usable" sign on the icon of CronniX. I opened the application, and it gave a message stating that this app can't be run on this architecture.
It seems Apple automatically creates some kind of badge on application icons if they're not capable of running on PowerPC machines. I don't think it's the same way on Intel Macs, because they can run PowerPC binaries in Rosetta.
[robg adds: The icon seen here is from the Parallels Desktop Uninstaller tool, which was the only Intel-only app I had handy that showed the "not usable" badge.]

