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If you don't like user interface sound effects in general (in any app), you can turn them off in the Sound preference pane in System Preferences. (Look for the "Play user interface sound effects" setting under the Sound Effects tab.)

But if you just want to eliminate that particular iCal sync sound, enter this command in a Terminal window:

Code:
defaults write com.omnigroup.OmniFocus SyncFinishedSound ""
To change it to use a different sound (e.g. the "Submarine" sound effect), try this:

Code:
defaults write com.omnigroup.OmniFocus SyncFinishedSound "Submarine"
To return to the factory setting:

Code:
defaults remove com.omnigroup.OmniFocus SyncFinishedSound
Hope this helps!