When Mufasa falls off a cliff at the halfway point of The Lion King, it's a devastating moment for both Simba and the audience, since Mufasa is a full-blown supporting character who is basically the second-lead for the first third of the picture. Yet the countless dead mothers in prior and future Disney animated films (The Little Mermaid, Beauty and the Beast, Aladdin, Pocahontas, The Hunchback of Notre Dame, Finding Nemo, etc.) merit at best a cameo in the prologue before being bumped off before the title card comes up (Bambi is the rare exception, where the doomed mother sticks around long enough to be mourned). Even The Princess and the Frog, another rare animated feature to spotlight a dead father and a living mother, makes a point to keep the deceased dad in the audience's minds throughout the narrative, including a climactic flashback that concludes Tiana's character arc. The recently deceased mother of Super 8 merits a photo and a name, while the dad in Extremely Loud and Incredibly Close is played by a major star (Tom Hanks) who has a supporting role throughout the drama despite dying on 9/11 in the opening moments. Bruce Wayne loses both of his parents in Batman Begins, yet it is only his father (Linus Roache) who gets a real character to play and more than one or two lines. It is his father whom Bruce Wayne holds as a role model and his father who Rachel Dawes (Katie Holmes) and Alfred Pennyworth (Michael Caine) constantly refer to when discussing Bruce's actions and his moral worldview. Martha Wayne is played by Sara Stewart, but that's all I could tell you about her.
There are occasional exceptions to be found. The Harry Potter series always emphasized the life of Lily Potter while detailing James Potter's school days. While Magneto loses both of his parents in a concentration camp in X-Men: First Class, it's clearly the death of his mother that scars him the most. But the general rule still applies. When both parents are dead, it's the father's influence that is most felt from beyond the grave. And while dead mothers are often mentioned but rarely seen, dead fathers often have featured roles pre-and-post death in their childrens' stories. Both March Webb (should be return to direct the Amazing Spider-Man sequel) and Chris Nolan (depending on if The Dark Knight Rises even remembers Martha Wayne) have a chance to buck the trend, and it will be interesting to see if either filmmaker takes or took the opportunity to expand the character of that 'other' dead parent. While losing a father may be some kind of alleged rite of passage in classical storytelling, losing a mother shouldn't be either ignored or used merely as a cheap ploy for emotion. If there is another Spider-Man film in this current universe, it would be nice if Peter remembered that he had a mother too.