Yes. You'll need to create a file called "fstab" in /etc if it is not already there:
sudo nano /etc/fstab
Next, we'll need the partitions Unique Universal Identifier (UUID). Open Disk Utility, and highlight the partition you'd like to no have auto-mounted. Then hit CMD+I and you'll be greeted with the following screen (notice the UUID highlighted):
We will then need to enter the following line into our fstab file. The following example will prevent my "Shockwave" partition from auto-mounting:
UUID=27C2148B-1734-3900-B89C-FE3EB7E11DBC none hfs rw,noauto
Hit CNTRL+O to save when you're done. You can add as many as you like; one per line. Reboot and those partitions specified in fstab will not be mounted.
The UUID is the partitions unique identifier (consult the man-page below if you'd like to use device's label instead). The noauto tag tells OS X not to auto mount on load. You can still mount them using Disk Utility, but OS X won't do it for you initially.
If you'd like to learn more about fstab and what you can do with it, you can view it's respective man-page.