I've used it since it first came out, on about half-a-dozen Macs of varying types – it's not caused me a single problem. I will say though all the Macs have been PowerPC – I've not tried it on an Intel.
The app is well safe and very much worth the money. Only time it is dangerous is if you have Candybar with a icon set applied and then load Shapeshifter (Apply it) with a built in icon set that comes with a theme, it'll make the current set of icons in Candybar overwrite Aqua default.
It can be fixed though, but if it happens to someone its handy to know...