I'm not a Gnome3 user and I installed it just to try, so I might be wrong, but I can't see anything, in the "System settings", to configure the behaviour of removable drives. I also looked in the Nautilus settings and it's the same (while Xfce's Thunar, for example, has a fine-tuning section in its preferences manager).
I would personally edit fstab (first making a copy of it) adding explicit entries for the partitions you'd like to leave unmounted. If you want to try this, first you'll need to get the UUID (universally unique identifier) of each partition and append it to fstab, using blkid (as root). For example, for an hypotetical /dev/sdc1 partition, type:
blkid /dev/sdc1 >> /etc/fstab
Pay attention to type >> and not > (otherwise you'll overwrite fstab instead of appending to it). Open fstab and you'll see something like this at the end of the file:
/dev/sdc1: UUID="D34TG678RGRT564" type="ntfs"
Now, clean the line a little bit, leaving the partition's UUID only, without "" :
Then complete the line adding a valid mount point for the partition, the filesystem type ("vfat" for FAT, "ntfs-3g" for NTFS), the "defaults", "user" and "noauto" options (the latter will prevent the partition from being automatically mounted) separated by comma with no spaces. Finally, set the dump and pass options to 0. The result will be like the following:
UUID=D34TG678RGRT564 /home/user/mnt ntfs-3g defaults,user,noauto 0 0
The line will affect that partition only, thanks to the UUID. You'll have to do the same work for the other partitions you want to control through fstab.