The e-mail facility provided with Google Apps is no different than Gmail. In fact it is Gmail with your own logo. It therefore includes all it's features.
The Key features are :-
Spam filtering: This is what saves all of us a mighty headache. It automatically defends you against spam, phishing, and viruses, and moves all these messages into the Spam folder. Which is deleted, once every month.
Storage Capacity: The next best thing is the large storage capacity of 25 GB for Premier Edition users. Standard Edition gets the normal 6 GB approximately.
Message Search: When you have such a large storage at hand, it obviously becomes quite a task to find and refer to an old but important mail. That's where the search function comes in handy. You just have to type the search terms into the search box and click "Search Mail". Include one or more search operators like "from: " or "to: " and limit the results to messages that meet these criteria. Not only that, you have the option of advanced search by clicking the link "show search options".
Message Conversations: Messages in continuation to every mail you receive or send is bound together as conversations in a thread. You don't have to look for all those messages scattered throughout your inbox, for all related mail are automatically grouped together as a conversation. They will show as a single line, but when you open the message it can be expanded to show the entire sequence.
Labels & Filters: You can label different type of messages you are likely to receive and organize them into sections. All personal messages will be archived into that Label. Labels are like folders where you may differentiate your messages. One can segregate the labels with colors too. You can also create rules called filters to automate things like archiving certain types of messages or applying labels.
Google Talk: The inclusion of Google Talk within the e-mail client is a very useful integration. If any of your contacts are online simultaneously, you can initiate a text, voice or video chat with them. Such chat conversations can be stored for future reference if needed.
Mobile Access: This feature can be configured with ease enabling access to your mail while on the move. Most smart phones are compatible.
Constant Innovation: Another thing one can rely upon is constant innovation. Very frequently new features and add ons are tested and deployed. Just when you start feeling the best is achieved, it gets better.