It doesn't hurt to occasionally make a tar.gz backup of your configuration files so you can go back and examine the previous version in case you clobber a configuration file during updating.
For most configuration files, I'll give it a quick scan, and usually replace with the updated package.
If I feel like I need to give the update a closer look, I'll usually use a program called 'meld' (dev-util/meld), which gives me a much more visually intuitive side-by-side comparison of the update with the original. There are several other programs which can also do a much better job of comparing/merging than the one built into 'update-etc'.
Gigabyte GA-P35-DS3L - Intel(R) Core(TM)2 Duo CPU E6750@ 2.66GHz
nVidia GeForce 7600 GS
2 GB RAM