The Control Strip
With the launch of PowerBooks, Apple added a tiny Control Strip for easy access to system controls on smaller, less capable mobile displays.
Apple Menu Items
Most of us have completely forgotten the original Apple menu was completely customizable. It was a place to put aliases for commonly-used apps, documents and folders for easy access.
The Scrapbook and Note Pad
The Scrapbook and Note Pad existed in the earliest versions of Macintosh operating systems, and were a particular kind of app called a Desk Accessory along with the calculator and other utilities.
The Scrapbook might have been ahead of its time. And if the simple Note Pad could see what has become of the modern Notes app, it might be proud.
Cyberdog
Cyberdog was a suite of internet software based on OpenDoc, which looked to replace the modern app/file metaphors with containers and editors. It was a confusing concept for many people, and even moreso with internet software, which was new territory.
The Cyberdog Notebook was a unique starting point for various internet tasks, but it was lost with OpenDoc.
Themes
With the arrival of the mp3, music software was almost universally theme-able – apps such as Audion and SoundJam allowed more ambitious designers to redesign how the software looked.
Afterwards, Konfabulator (eventually bought by Yahoo) came along, creating a playground for designers and programmers to create all kinds of useful widgets, which did not have to follow to any preset design guidelines. Apple responded with the Dashboard, which was eventually replaced with the widgets we have now.