The obvious place to start is with Bible films that cover the story of Cain and Abel. There are a good number of these going all the way back to 1911's Cain et Abel through to a brief cameo is 2009's Year One (pictured). Aside from those two others really stand out. Firstly there's Huston's 1966 The Bible: In The Beginning which has a visceral primitive quality about it. The other is from 2003's The Real Old Testament, which has some great lines in it. "I like Nod. Nod is great" and (on the mark of Cain) "Y'know those kinds of things are just so complicated that..."
Cain and Abel is such a prominent story that it's tempting to just leave it there, but there are a few other stories of (potential) fratricide in the rest of Genesis. Firstly you have Jacob and Esau, which whilst the story itself ends on reconcilliation echoed down the ages and seems to have played a part in the subsequent conflicts between the Hebrews and the Edomites (c.f. the famous verse in Malachi 1:3). Sadly no Bible film that I can recall covers this conflict.
The second is also more about fratricidal intent which manages not to avoid in murder - Joseph at the hands of his jealous brothers. Again Joseph hasn't featured in a huge number of Bible films, although the Emmy award winning entry for "The Bible Collection" series, starring Ben Kingsley, stands out amongst television (and as the emphasis for the EBR is on reception rather than specifically film that should be fine). And of course there's the Lloyd-Webber thing. Incidentally both of these passages are evoked in consecutive chapters of Paul's letter to the Romans (8:28-9 and 9:13), although the first doesn't use a direct quotation.
Finally there is the story of Hamor and Jacob from Genesis. Whilst the Bible doesn't really make it clear how closely Jacob and Hamor are, the story as portrayed in the 1998 Malese film La Genèse emphasises the "brotherly" nature of the relationships between the heads of the different tribes and clans. Furthermore once Hamor's son Shechem marries Jacob's daughter Dinah then the two men become related, through partaking in Hebrew ritual as well as marriage. The subsequent murder of Shechem by Jacob's sons more than touches on fratricide.
But aside from Bible films there are other, more contemporary films which explore the issues. Perhaps the most well known film to draw on the resonances of the Cain and Abel story is East of Eden starring James Dean (1955). The two brothers (Cal and Aron) squabble over their father Adam's favouritism as well as a woman they are both attracted to. Whilst the film does not end with fratricide, many of the same emotions are thrust under the microscope, and the film deliberately nods in the direction of the Biblical narrative.
Another film that has been linked to the Cain and Abel story is Milos Forman's 1984 Amadeus which has been likened to the Cain and Abel story by Gregory Allen Robbins.
Lastly, there is the TV series Kane and Abel (1985). I've never seen it although I remember my parents being taken with it when it aired on TV. Whilst the Kane and Abel here aren't brothers, there's a sense of brotherhood rivalry between the two men which draws additional mythical power from the similarly named biblical story.
The future actually promises a couple of further possibilities. Firstly there's rumours of Will Smith starring and producing a vampire take on the ancient story, likely to be called The Legend of Cain. There's also Warrior a cross between the story of Cain and Abel and that of Rocky. Actually that was released in September last year (2011), but I missed it then and haven't had a chance to catch it yet. I'd be interested to know what anyone who caught it thought. I notice it's currently sat at 145 in the IMDB top 250.