I have just tried to change my font size in Eclipse 3.6.0 in the following way:
General → Appearance → Colors and Fonts → Java Editor text font
However, the font size only changed in the file I had open. How can I change the font size for all Java files and projects I open in Eclipse?
If you are changing the font size, but it is only working for the currently open file, then I suspect that you are changing the wrong preferences.
Check that you do not have per-project preferences. These will override the top-level preferences.
Per comment below, this has moved to the Eclipse Preferences menu (no longer named the Window menu).
The Window menu is live again, that is, menu Window → Preferences.
Note Be sure to check out the ChandraBhan Singh's answer, it shows the key bindings to change the font size.