The sound is intended to mean "I'm finished syncing". You can disable it by turning off "Play user interface sound effects" in System Preferences. However, OmniFocus won't notice the new setting until you quit and restart.
Alternatively, you can disable that particular sound in OmniFocus using this Terminal command:
Code:
defaults write com.omnigroup.OmniFocus SyncFinishedSound ""
(To run a defaults write, just open Terminal app, then paste everything in the codeblock above into the window as a single line. Hit return, then restart OmniFocus.)
Hope this helps!