CLR is fine as long as you rinse it off thoroughly. Of course, you can't use it *in* your tank.
And I don't know if I just got a bad batch, but when I tried CLR it did NOTHING. I even poured it on my skin and it didn't burn, it might as well have been water. Other people say it works great, I don't know what the deal is.
A gentler treatment is covering the glass with paper towels, then soaking with vinegar. Rub down the paper towels to remove air bubbles. Let sit. Don't expect this to fully remove deposits or be effective on heavy deposits, but it is a great pretreatment for the best remover in the world...
Razor blades. As found in hardware stores, for scraping anything that needs to be scraped. As long as you keep the blade at an angle, the glass wet, and refrain from digging the corner of the blade directly into the glass, it will not scratch. The vinegar pretreatment makes the job easier by softening the deposits, but it's not necessary. In fact, you can use the razor blade IN your tank. Use the common, cheap, steel blades, don't try and get fancy and use a carbide scraper - that will scratch the hell out of glass, no matter how careful you are.