In my A1200 I use an SD card for HD and from time to time, usually every two months, I do a full image of it on my Linux Machine. The good thing with this method is that you can restore the whole HD two as many SDs you want. Also, you can easily mount it into an emulator (WinUAE, FS-UAE etc) and make changes there if needed.
The downside is that it takes a lot of space. Mine is 16GB, so it takes almost the same space on my hard disk. But because the data it contains are not crucial, I delete the previous backups, as long as I am sure that the new one is working.
For my AmigaOne's I use git for all my development projects and commit all the latest changes every time. Other than that, I use a second hard disk where I sync all the apps and system.
