Second Today - allows you to run a today screen in addition to TF3D. Useful if you have some today plug ins that you want to use together with manila. Without second today, you would have to disable TF3D in order to use the today plugins.
Elite force Lumos - is an app that automatically controls the backlight brightness. The built in software of the HD is not very good and for me does not dim the display enough in dark rooms.
Tocuh response - give a vibration when the screen is pressed. Fully configable - ie duration of the vibration, whether it should only vibrate on the keyboard etc. I found that the HTC vibration for keyboard etv was too much. It also gives you feedback when touching other parts of the screen (standard HD willl only give you feedback on the keyboard.)
Hope this helps.