From a security and reliability standpoint, it's better to have separate hard disk partitions for directories that are large, and especially to separate those which are frequently-changing (/tmp and /var) from those that can be mounted read-only except when installing software (/usr). Some people also make separate partitions for /home and /usr/local. Separate partitions mean that if one gets corrupted, the others won't be affected. It also means you can mount some partitions (especially /usr and /boot) read-only except when doing system administration: this decreases the likelihood of corruption or mistakes dramatically. Don't do the distribution default, which is usually to put everything in one partition. Of course, you can go overboard if you use too many partitions, and if you don't anticipate your sizes correctly you may end up with wasted space in some partitions and not enough space in others. In that case you'll either have to back up the files and repartition, or use symbolic links to steal space from another partition. Both strategies are undesirable, so think beforehand about how many partitions are appropriate for this machine, which directories contain irreplaceable data, and leave some extra space for unexpected additions later.
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