Yes, it shows you've researched the company and showing their logo alongside your logo in a presentation does enhance a feeling of corporation.
Whatever you do, treat the logo with respect. I once saw a presentation from an advertising agency titled: "Brand wars. Is your brand buried in the clutter?"
They showed a whole heap of logos, all stacked on each other in a heap, with the clients logo hidden in between these logos.
The CEO of the company was present in the meeting (I don't think that was expected) and took offense.
Treating the logo with respect can avoid an emotional reaction. Remember, we aren't always rational creatures and we must respect each others emotional attachments.