Auto popup/down of the serial monitor seems to be popular.
Ability to put your own library files in a directory outside of the arduino installation so you can upgrade to a new release and keep your own libraries.
There is a list of libraries in the reference. Some libraries are included with the Arduino software. Others can be downloaded from a variety of sources. To install these third-party libraries, create a directory called libraries within your sketchbook directory. Then unzip the library there. For example, to install the DateTime library, its files should be in the /libraries/DateTime sub-folder of your sketchbook folder.