Can you make OSX mount just certain partitions when you connect an external HDD?

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.

You can add entries in /etc/fstab to prevent volumes from mounting. This is similar to the technique @cksum describes. Here are some example one-liners. They will create an fstab file if it doesn't exist, otherwise they will append. You need admin privileges.

1. Prevent an HFS (Mac) volume named Archive from mounting. If it is mounted manually, it will be Read/Write.

   echo "LABEL=Archive none hfs rw,noauto 0 0" | sudo tee -a /etc/fstab

2. NTFS volume named BOOTCAMP. Read-only.

   echo "LABEL=BOOTCAMP none ntfs ro,noauto 0 0" | sudo tee -a /etc/fstab

3. FAT32 volume named PMBPORTABLE. Read-only.

   echo "LABEL=PMBPORTABLE none msdos ro,noauto 0 0" | sudo tee -a /etc/fstab