I've never really been convinced of the comparison with McCartney. Everytime I've heard echoes of The Beatles in Neil's music its been similarities to John. I agree with others on "Kill Eye", "In My Command" and "NTGYTYA", especially the latter. And then there's "Last Day Of June" and "SWHHW" where vocally I think he's uncannily like John. "SWHHW" even employs a similar delay effect that John liked to use.
Also "Try Whistling This" and "Addicted" both remind me slightly of solo Lennon, parts of the piano-playing echoing "Jealous Guy" and "God".
More than the songs themselves though I think its the qualities in Neil's voice that bring out the comparisons. He has that slightly rough, intimate quality to his voice that John had and both can convey genuine emotion in a more subtle way than most singers when required.