Free Wireless Downloads
This doesn't sound like a big deal at first, most people don't mind downloading a book to their computer and then transferring it to their ereader, but once you get started with wireless downloads you find it's much faster and easier without all the extra steps.
Some ebook readers come with web browsers for surfing the internet, so that's something to consider too. Examples include the Kindles, Nook, Apple iPad, Pandigital Novel, and many others.
Some devices come with 3G wireless and others just have Wi-Fi.
To Touchscreen Or Not To Touchscreen
It is likely that touchscreens will eventually become one of the standard ebook reader features, but for now it is something that not all devices have. There are several types of touchscreen ereaders. Some touchscreens work with your fingers like Sony's touchscreen ereaders. The other type uses a Wacom tablet or similar technology that requires the use of a stylus.
And then there are the tablets with either resistive or capacitive touchscreens. Capacitive screens require a lighter touch and are easier to use, but resistive screens are getting better all the time.
Some issues with touchscreens are fingerprints and reflections. There are screen protectors to help with this.
What is comes down to is this: Ask yourself what's more important, text contrast and clarity or touchscreen with on-screen highlighting and note-taking. And if you go with a Wacom, consider the fact that you'll have to use a stylus to utilize the touchscreen capabilities.
Screen Size and Portability
Most ebook readers have 6-inch screens (measured diagonally), to maximize portability and readability, but there are a growing number of different screen sizes hitting the market lately.
5-inch screens are becoming a lot more popular, with several new pocket-sized devices being released by different companies.
For larger devices there are 7.1, 8.1, and 9.7-inch screens, and the forthcoming Plastic Logic looks to have a screen size larger than 10-inches. These are more suited for reading large PDFs, newspapers, textbooks, and business documents.
Annotations and Fonts
A few ereaders allow for note-taking and highlighting text. With the Kindle you control a cursor and the 5-way navigation controller and type notes with the mini-keyboard. With Sony's touchscreens you simply write and highlight directly on the screen and type notes with an on-screen keyboard. The Nook uses an on-screen keyboard and navigation arrows in the LCD section.
All ereaders offer different levels of text size, but only a few allow you to customize font-type without hacks.
Reference
A dictionary feature is important for some people, and most ebook readers offer this nowadays, but not all.
The devices with wireless access can easily search Google and reference sites like Wikipedia.
Text-to-Speech, Audiobooks, and Music
Only a handful of ebook readers offer a TTS feature: the Kindles, BeBook Mini, EZ Reader Pocket PRO, and Hanvons.
A number of devices allow for listening to MP3s while reading. A couple of devices have built-in speakers (listed above), and others just have a headphone jack for listening to audio.
The Kindle can play audiobooks purchased from Audible.com. And other devices that support MP3 files can get audiobooks in that format from places like BooksOnBoard.