Sony NEX-3 vs Fujifilm S1

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Larger sensor
APS-C vs 1/2.3 inch
More sensor area. Bigger is (generally) better.
Bigger pixels
~ 5.16 vs 1.34 microns
Better low-light and dynamic range (all else equal)
Thinner
33 mm vs 110 mm
Thinner
Bulb shutter
Bulb vs No bulb
Hold the shutter open manually for long exposures
Bigger JPEG buffer
38 vs 9 shots
Take more JPEG shots before waiting (burst mode)
Faster shutter
1/4000 vs 1/2000 sec
Shoot wide open in bright light

Focus peaking
Peaker vs Non-peaker
Your camera will highlight what's in focus
Less expensive
$500 vs $600 (MSRP)
Save money for lenses or accessories
Tilt-swivel screen
Tilt-swivel vs tilt-only
Tilt and swivel the screen for maximum shooting flexibility
Eye-level viewfinder
Eye-level vs Rear display only
You'll be able to frame photos even when the sun is out
In-Camera Image Stabilization
Yes vs No
Reduces the effects of camera shake at slower shutter speeds
Built-in Wi-Fi
Wi-Fi vs None
Share your photos wirelessly
Internal flash
Internal flash vs None
Useful in a pinch for fill flash
Shoots 1080p video
Yes vs No
You'll want this if you shoot video
Less shutter lag
0.13 vs 0.44 sec
Focus and take a photo quickly (wide angle)
Shoots 60p video
Yes vs No
A faster framerate can give you more editing options
Faster JPEG shooting
9.6 fps vs 2.7 fps
Faster JPEG shooting (burst mode)
Slow-motion videos
Yes vs No
Shoot slow-motion videos

Rear display
Both provide
Review photos on the back of the camera
In-camera panoramas
Both provide
Stitches multiple shots into a panoramic photo
RAW file ability
Both provide
Gives you more flexibility to develop your photos later
Manual focus
Both provide
AF is for the weak. Real photographers focus manually.
HDMI out
Both provide
Use HDMI output to monitor or review video
Hot shoe
Both provide
Off-camera flashes open new possibilities

Touchscreen
Neither provide
Interact with your camera just like your smartphone
Built-in Bluetooth
Neither provide
Always-on wireless connectivity
Built-in GPS
Neither provide
Geotag your photos
On-sensor phase detect
Neither provide
Usually improves live view and video AF performance
Top deck display
Neither provide
Check settings with a screen on top of the camera
Integrated ND filter
Neither provide
Shoot in daylight with a large aperture or slow shutter
External Mic Jack
Neither provide
Improved sound fidelity when shooting video
Dual card slots
Neither provide
Gives you more storage flexibility
Headphone jack
Neither provide
Monitor audio recording while you shoot video