In the laptop mode config file, you can choose for it to not control the HD spindown time, if that is something you are worried about. The config file is actually very well documented and can be found at: /etc/laptop-mode/laptop-mode.conf. The specific option you are looking for is "CONTROL_HD_TIMEOUT". Setting that variable to 0 should prevent laptop-mode from setting the spindown time of your disk.
Also, linux can do some pretty amazing power management (far beyond what laptop-mode offers by default) but, it's just harder to setup. Some good places to start are the powertop tool and www.lesswatts.org. To install powertop and run powertop you can do the following from a terminal:
sudo apt-get install powertop