Several differences have been noted between the tracks on this compilation from the original released versions of these songs:
Miss Sarajevo: This is not the album version, nor the single version.  This is the radio edit version previously found on only promotional singles of Miss Sarajevo.
Mysterious Ways: There is an alternate vocal in this version of the track. At 1:35 min the line 'She's the wave, she turns the tide, she sees the man inside the child' has been changed to 'She's the wave, she'll turn the tide, and no question, she knows why.' Likely mastered from a different vocal track.
Numb, Discotheque, Staring at the Sun, and Gone: All are new mixes of these tracks done specifically for this compilation. Gone also features a slightly different lyrical track from the original version.  In the Best of version the line "What you thought was freedom just was greed" is different from the original "What you thought was freedom is just greed".