Oh, yeah - I'm sure he could pick a different favourite for every day of the week (couldn't we all?). I was reading 'Mozipedia' by Simon Goddard and it quotes Marr as saying that 'the title alone was worthy of a single', and that he wore the tape out from playing it in the car so much. In recent years I've also heard him name "Hand in Glove", "Stop Me..." and "How Is Now?" as his favourites, but I expect he loves them all. Someone once asked him on Twitter which one was his favourite, and he said something like, "Sheila Take A Charming Bigmouth Barbarism Panic"
He also said in the early 2000s that hearing the vocal being put to "I Know It's Over" was one of the highlights of his whole career.