There are certainly some things to say about the religious themes in Spider-Man 3, but most of them have been said elsewhere already. In addition to the review by Holy Heroes' own Sci-Fi Catholic, I found some intriguing reviews (of varying depth) on BeliefNet, The American Papist, The Dallas News' religion blog, and BeliefNet again. There's even a Bible Study Guide for the movie, written by Craig Detweiler of the Reel Spirituality Institute. The reviews tend to focus on the film's sin/redemption themes, and I don't have too much to add to those points. (Though I should probably add that many of these reviews are a little overly kind to the movie's many faults, such as the fact that those self-same redemption themes are occasionally shoehorned in at the expense of coherent characterization.) So instead of talking about those well-discussed themes, I'll give some background on one of the key moments in defining the film's religious landscape: the bell tower scene.
Here's what Spider-Man 3 gives us: our hero, who has been turning into an insufferable jerk on account of being possessed by alien goo, goes to a church steeple to brood. (In movieland, it's probably supposed to be a Catholic church. But sharp-eyed New York-savvy viewers will note that the exterior is actually Grace Church, which is Episcopal. Not that it matters much, especially since the interior is another church entirely.) And lo and behold, his rival Eddie Brock, another insufferable jerk, has picked precisely this moment to go to the same church to pray for Peter Parker's untimely death. As the bells toll, we discover that the aforementioned alien goo really, really doesn't like loud noises (or at least not church bells), and Parker is able to separate himself from the evil symbiote, just in time for it to descend the bell tower and answer Brock's prayer.
This scene is lifted more-or-less directly from the pages of Web of Spider-Man #1 (1985) and Amazing Spider-Man #300 (1988). Web #1 (written by Louise Simonson with art by Greg LaRocque and Jim Mooney, and a truly incredible cover by Charles Vess) was the original conclusion to the saga of the alien costume, and it's interesting to see that the story concludes with the same sort of redemption motifs we see in Spider-Man 3. In this story, Spidey enters the bell tower of a yet-nameless church during a battle with some C-list villains (The Vulturions, if you must know), and the sound of the bells separates the costume from him. But separation from the symbiote, combined with the overwhelming sound of the bells, nearly kills Parker himself. The costume, in its final moments, redeems itself by pulling Parker to safety before finally disappearing in a puff of smoke. As the costume took control of Parker, it absorbed some of his humanity and compassion, and in its final moments it atones for its sins.
...OR DOES IT?
It turns out the question of why the symbiote saved Parker does not "haunt him for the rest of his life," as the final caption in Web #1 states. In fact, it was retconned out of relevance three years later when Venom was introduced in Amazing #300 (written by Dave Michelinie, with art by the anatomically-challenged Todd McFarlane). The symbiote did not, in fact, die in the church (now dubbed, somewhat generically, "Our Lady of Saints"), but simply rested their, recuperating until another suitable host appeared. It finds such a host when Eddie Brock, a Catholic newspaper reporter who became a laughing stock over some shoddy reporting on the Sin Eater case*, goes there to pray about his desire to commit suicide. Like the film's Brock, Venom's appearance answers his prayer—but the religious symbolism doesn't end there as they do in the film. When Venom finally traps Spider-Man, the manner in which he attempts to kill his rival takes on a decidedly liturgical tone. Webbing Spidey inside the bell that had allowed him defeat the symbiote three years prior, Brock transforms the costume into a priest's robes.
It's tough to say how much significance there is to the religious trappings of this scene—are Michelinie and McFarlane trying to make some greater point about the misuse of religion for violent and worldly ends, or are they just being ironic? In any case, Venom's origins are rooted in religious symbolism that survived the transition to the big screen. (Too bad we can't say the same for the characterizations of, oh, the entire supporting cast. But that's another can of fish that I won't get into here.)
*You think this origin is convoluted? Don't get me started on Cable.