There have been a few times when Transformers has made references to this. In #1 of Transformers Armada, in this panel, the text that keeps repeating itself on the monitor behind him are, "All Your Base Are Belong to Us," and "If you can read this you are obsessed." The scan isn't clear enough, but if you take out your copy of #1 and have a close look you can just make it out. In Transformers Rescue Bots there's a virtual character called CAT who also says, "All Your Base Are Belong to Us."

All Your Base Are Belong To Us