The Eclipse-Fonts extension will add toolbar buttons and keyboard shortcuts for changing font size. You can then use AutoHotkey to make Ctrl+Mousewheel zoom.
Under Help | Install New Software... in the menu, paste the update URL (http://eclipse-fonts.googlecode.com/svn/trunk/FontsUpdate/) into the Works with: text box and press Enter. Expand the tree and select FontsFeature as in the following image:
Complete the installation and restart Eclipse, then you should see the A toolbar buttons (circled in red in the following image) and be able to use the keyboard shortcuts Ctrl+- and Ctrl+= to zoom (although you may have to unbind those keys from Eclipse first).
To get Ctrl+MouseWheel zooming, you can use AutoHotkey with the following script:
; Ctrl+MouseWheel zooming in Eclipse.
; Requires Eclipse-Fonts (https://code.google.com/p/eclipse-fonts/).
; Thank you for the unique window class, SWT/Eclipse.
#IfWinActive ahk_class SWT_Window0
^WheelUp:: Send ^{=}
^WheelDown:: Send ^-
#IfWinActive