There could be many things to say about Tarkovsky and his films. The most important (which could be found in many comments ) is that he does not offer us a very clear interpretation , leaving us to guess, wonder and question ourselves.
My interpretation of this film is that the whole trip to the Zone and to its core, the Room its a metaphor for the dangerous trip the human soul takes in searching the redemption and finally the Kingdom of Heaven. Stalker (like Jesus) is the one who shows the way to this kingdom - and there are some arguments to this idea. First, before entering the dangerous Zone, he lies on the grass thinking (or praying?), just like Jesus did in the garden of Ghetsimani before being crucified. Stalker is the one who shows who could reach the final point of this trip: not the good or the bad, but the desperate ones. Stalker is the one who fights with the professor (another metaphor for the rational and logical part of our minds) who wants to destroy the Zone, and also Stalker is the one who in the end laments over the lack of will people have to enter the Zone and to believe in its powers.
There are so many powerful shots in this film and I choose only some who really got to me: 1. the destroyed tanks in the first part of the trip are for me the communist weapons who tried to destroy the faith and the church in Russia and in the other communist countries. They failed. 2. the objects shown in the water when the 3 heroes sleep near it, the money, the weapon, the tiles under the water describe the precarity of our material world. 3.the water in the film, from the beginning until the end - it is pure poetry. 4. one dialog between the writer an Stalker, the writer is saying: "who needs your room, i don't need your room" - it reminded me the dialog between Ivan Karamazov and Alexei Karamazov, the first saying to the other: "I don't need your God"
But this is only one interpretation, and if it would be the only one, we would not be talking about a great great film.