I can't answer this question, as to me there's no real 'best song' or 'greatest' anything... That's just my opinion, there's too much of everything out there (and being made) to really apply such a label to anything in particular.
I will, however, list some of my favorite songs that come to mind at the moment, in no particular order:
Pink Floyd - Learning To Fly
One of the most beautiful songs ever, in my opinion.
Judas Priest - Angel
I absolutely love this song's lyrics and the way it slowly builds throughout.
Korpiklaani - Happy Little Boozer
Because it's one of the most infectious and catchy songs ever written.
Luca Turilli - Mother Nature
Amazing vocal melodies and performance. The new female singer has an incredible voice-- very natural and almost effortless sounding.
Mnemic - Sane vs Normal
Strange as it sounds, it reminds me of the game Killer 7-- That being one of my personal favorite games, I love this song.
Other mentions are Comfortably Numb, The Trial, and Brain Damage/Eclipse by Pink Floyd. Also, The Unforgiven by Metallica. Yeah, so sue me... I thought the ballads were the best part of The Black Album.
I could go on for ages, and some of these may change, but some of the songs in that list are timeless classics to me for whatever reason, and will probably stay among my favorites. I know I forgot a whole bunch, but hey, it's a difficult question.
Also, I just realized all of my picks are from fairly well known bands... There's tons of obscure songs/bands I could list, but I guess sometimes there's a reason something becomes well known.