I agree, I know I’m biased as a Floyd fan, but I cannot understand why Wish You Were Here and Comfortably Numb aren’t in the top 100 at worst, both are total classics by most standards, and there’s nothing from DSOTM - surely at least one of Time, Money, Us And Them or The Great Gig In The Sky could have made the list? This is made more galling by the presence of Another Brick In The Wall Part 2, which I like but is overrated (I think it's position is fair, however). I agree about Led Zeppelin too, where are Dazed And Confused, Over The Hills And Far Away or When The Levee Breaks? I do think they get a fairer deal on the list than Pink Floyd, though (e.g. Ramble On and Heartbreaker do make the list, whereas Floyd’s plight is akin to Zeppelin only getting Stairway, Kashmir and Whole Lotta Love in the top 500).
Another band who always get treated unfairly by Rolling Stone are Dire Straits (they’ve never been inducted in the Rock And Roll Hall Of Fame, for instance), again I’m a fan but I fail to see why Sultans Of Swing shouldn’t be on this list – great guitar, great lyrics and an all round classic track. I can understand why they want to recognise post-2000 material, but to see Sultans excluded for the likes of Umbrella is a crying shame.
There’s also the issue of tracks by the same being ranked unfairly relative to each other – taking U2 (a band I like but another who I think RS tend to favour, are all their songs on the list truly top 500 worthy?) as an example I think New Year’s Day (#435) is a better song than Sunday Bloody Sunday (#272). However, speaking of U2, I noticed that my own favourite Where The Streets Have No Name is missing, while Pride and Beautiful Day made the list.
There’s other problems too, I think the Beach Boys have been overrated somewhat – I wouldn’t disagree with the inclusion of songs like God Only Knows, Good Vibrations or In My Room but I really don’t see how California Girls by The Beach Boys can justify being in the top 100, it’s never stood out to me as being one of their best songs and the lyrics make me wince. I like Sloop John B better, but I don’t regard it as a great song either, and although both are very nicely sung I think they are hardly top 500 songs.
I do like Bob Dylan, although I can’t help but think someone like Neil Young, who doesn’t have a song in the top 100, gets a bit of a raw deal by comparison (Southern Man or The Needle And The Damage Done, anyone?).
I can’t say I think much of their top ten, the first one I’d remove is Hey Jude which in my opinion is well overrated (I’d like this list a lot more if this was swapped with one of the aforementioned Pink Floyd songs). Also, I suspect I’m not the first to notice this but there’s something a bit fishy about the choice of top two songs as well...