Depends what you need.

My list would be, in order of importance and why:
Openmode - To get rid of aegis and the cat and mouse game of updating refhashlist, when certain files in /etc are modified.
N9-button-monitor - To use led flashlight when the device is idle.
Rotation patch by vesuri - To enable rotation in select apps and multitasking view.
Drive/Maps patch - To enable traffic information in Drive.

And other stuff which could or not be called modifications depending on your point of view such as enabling ssh key based login for user, adding more complete $PATH for user and installing busybox-power.