What does John 12:6 mean?

Judas has criticized Mary's act of sacrificial worship: using up most of her life savings, in the form of an expensive oil, to anoint and honor Jesus (John 12:1–3). His critique is phrased in a very logical way, noting that she used up 300 denarii worth of resources. This was the equivalent of almost a year's wages for the common laborer. It's a fact beyond argument that such a sum could have been used to feed many poor people. As others nod in agreement (Mark 14:3–11), he complains that this was a waste.

This verse explains the real motivation behind Judas' reaction, almost certainly one that John did not realize until after Judas' lies were found out (Matthew 27:3–7). As the group treasurer, Judas was able to skim money whenever he wanted. The "waste" he sees here is money that could have gone into his own pocket being poured onto the feet of Jesus.

Judas' motivations here are especially crude. However, the tendency to snipe at the service of others is common, even if there is an element of fact to be argued. When someone does "too much," according to another's opinion, the assumption is always that it's a "waste." To be fair, maybe some of those acts are wasteful—but that's a judgment to be made by God, through His knowledge (1 Samuel 16:7), and not ours (John 7:24). When others are sincerely led to give or sacrifice or serve, we should focus on honoring their intentions, rather than grousing about what we would have done differently.

Jesus will defend Mary in the next verses, noting these are unusual circumstances (John 12:7–8). His reference to the fact that "the poor you always have with you" is not a dismissal of poverty, but a statement of fact: these are the last moments Jesus will be with friends like Mary, Martha, and Lazarus.