There is no one single greatest camera for every situation. Learn that now, if you haven't already. It takes the director and cinematographer discussing in great detail how and even why they are shooting a film to decide which camera will best suit their needs. Need a run and gun, lightweight camera that's easy to carry handheld? The FS100 or a RED camera is not going to be your friend. (The FS100 is not very ergonomically sound and the RED camera requires a rig or sticks, even standing still because it is so large.) Need a full frame camera that can shoot 60fps in full 1080? Canon 7D may be the cheaper option, but it's not going to give you what you need. However, you may sometimes find the perfect camera for your situation and it becomes magic on the big screen.
Take for instance the recent Oscar winner, Dallas Buyers Club. Vallee was determined to shoot in completely natural lighting for this very short 25 day shoot. He also wanted the option to shoot in a full 360 degree set. Not inhibiting the actors from moving into certain areas of the set was very important. So, let's look at the needs. We need a camera that doesn't need a lot of light, is lightweight so that it can be moved by hand on a whim, and capable of delivering Hollywood quality images despite these limitations.
Dallas Buyers Club was eventually shot on the ARRI Alexa digital camera. First of all, the Alexa can shoot for 4K resolution. That's a huge plus for filmmaking in a time where formats and resolutions are getting higher and more competitive every second of every day, even in the consumer market. The next perk of this camera is the full frame CMOS sensor, which is capable of shooting in low light with minimal noise and makes the digital images look like they were shot on film. PERFECT, right? It's giving the filmmaker a high resolution with minimal exposure needs. So what's next? Well, the Alexa has a handle for easy whipping around, a viewfinder in a place that makes sense for handheld shooting, and can be attached to a variety of mounts sold by ARRI and camera accessory companies.
So far this camera is looking perfect for Dallas Buyers. It's got all the needed features and it provides easy workflow as well as synced sound with its XLR inputs. But what about your low budget indie film? Well, an ARRI Alexa starter kit is going to cost you $80,000. (Link below)
Classic ARRI Alexa Starter Kit
If your whole film budget is ten grand (or even less), there's no way in hell you're getting an Alexa for that film. So what do you do? Well, you've got to compromise. But compromise doesn't mean death. Beautiful, award winning films are shot on Canon DSLRs and HDVs all the time; the camera operator just has to know what they're doing. Here's an article on the Mark II, if you're interested in it.
Canon 5D Mark II Has Made Itself a Home in Hollywood
In case you didn't read it, the article let's the cat out of the bag that parts of Captain America were shot with the 5D and intercut with the rest of the film like a gem. Of course there are downsides to the 5D, which you pay for in the price reduction: no synced sound, some operators feel it is harder to focus, and it's sensor is made for still photography so even though it is a full frame sensor, it's still going to be inferior to the Alexa to those who can spot the difference. But it's better to get your film shot on a Canon DSLR than to never make it because you're holding out for an Alexa.
So the answer is, there is no "best" camera. Every camera is going to have its perks and its faults, and yes, that fault may be the price tag. Be smart when picking your camera and by all means do what's best for your film and budget.