I know that you can only have 4 primary partitions on a hard drive. But if you're using less than 4, is there a benefit/penalty for using logical partitions?
Today, it doesn't really matter if you use primary or extended partitions.
There have been times where /boot had to be a primary partition but this isn't true any more. Also earlier incarnations of MS Windows required that you installed Windows to a primary partition.
When I set up a new disk, I make the first partition primary and put /boot there and put the rest as logical partitions into one big extended but this is just a personal preference.
I would say that there is indeed some penalty if you use logical instead of primary partitions:
So if you have up to 3 partitions keep them primary. If you have 4 or more, use the 4th as extended partition and start using logicals.