Honestly, the easiest and most assured to work when you need it method is to live clone the running SD card.
How you do that depends on the OS version.
If you installed Jessie with the LXDE desktop there is a built in SD Card Copier utility accessible through the gui. I don't know about other Jessie desktops but I'd be surprised if they all didn't acquire that tool.
All you need is a second SD card and a cheap USB card reader, run the Copier utility, pick the source and go. When complete, shut down the RPi, remove the old SD card and stick in the new one, power up and go. Now you have a known-good backup.
For Wheezy I used to go through the cloning process manually but eventually found a good/easy to use cloning utility on Github at
https://github.com/billw2/rpi-clone
After installing the package, stick an SD card in your reader, plug it into the RPi, then launch rpi-clone:
$ sudo rpi-clone sdc -f -v
The -v verbose switch will give you something to watch while the cloning process is running. Leave out the -v switch and the console will just sit there while the process is churning away, providing you with no clue as to progress until it's done.
Anyway, that's about it. I use both of these between my Jessie and Wheezy systems and they just plain work.
The one other thing I do is to have my "production" systems automatically push copies of any databases or important log files up to a NAS drive each evening at midnite.
For the most part those are the only important files that change with any real frequency, so if a system craps out tomorrow and I stick its backup card in, I can easily bring that system back to the last checkpoint.
Of course if I do a significant update to a system, once it has run long enough to prove it's still stable I'll do the clone thing again.
The amount of time a solid backup can save is staggering when you think about it...
Cheers!