Eclipse Neon (4.6)
Window > Preferences
General > Editors > Autosave > check Enable autosave for dirty editors > choose the value for autosave interval (in seconds)
Details in M7:
Auto-save of dirty editors is now available in Eclipse. The autosave option is disabled by default. A new autosave preference page (Preferences > General > Editors > Autosave) is available and allows to enable/disable the autosave and change the interval of autosave. The countdown is reset on keyboard activity, mouse click, or when a popup is displayed (e.g. content assist, preference page, …).