It shouldn't matter which queue you go through; most people don't know this, but UKBA officers are actually required to process everyone who comes up to their desk, regardless of whether or not they are in the right queue.

However, you would be well advised to present appropriate evidence of your Portuguese nationality regardless of which queue you are in. Presenting a Canadian passport might lead to the erroneous assumption that you have limited leave to remain in the UK, and might in extreme circumstances even lead to your refusal of entry, despite having the right to be admitted due to your EU citizenship.