Yesterday I've announced that I'm working on automatic logon to SAP systems on Eclipse. Today the changes in the plugin ABAP Extensions for Eclipse are published and you can use the first version of the automatic logon on your installations.
ABAP Extensions plugin you can find in Eclipse Marketplace or by doing direct installation from this link http://abapblog.com/eclipse/plugin/ABAPFavorites/ or by using the install button which you can find on the right side of this page.
After installation of update will be able to set the preference if you want to do automatic logon at start of Eclipse and if you want to logon automatically only to the systems, for which you have stored the password already. These are also default settings for the plugin. The logon happens in the background job. So if you have several systems in your workspace, it will take a while to logon to all the systems. The progress you can follow in the Progress View.
Beside the preferences page a new view is added in the ABAP category called Passwords. Here you should find all your systems clients and users.
The purpose of having here a tree is to have a possibility to store more than one mandant/user for the project and allow you to do right click and select the user with which you want to logon.
If you double click on the user name, you'll get the popup with the possibility to put the password in.
The popup is very simple to use. Once you enter the password, you can choose if you want to store the password in plain text or encrypted.
If encrypted, then on the Passwords view and in the Secure Storage preferences, you'll not be able to see the stored value.
If you decide to store it with the plain text, you will see it always.
When you right-click on the project node, you are able to add new client to the list.
When you right-click on client node, then you can create additional users or you can delete the client node.
When you right-click on the user node, you'll be able to use the credential to do the logon (without chaging the project data).
If you are already logged into the project, you'll have possibility to decide how to continue ( to log with new user and close all tabs of the project, or to cancel the action ). 
If you don't want to logon to all systems at eclipse start, then you can always logon with stored password using the command "Logon with Secure Storage" from the ABAP Project context menu.
Have fun and wait for more updates in this plugin ;)
