1. The sensor and thus image quality are the same, but the prices have a 21% difference! Video recording wise, for the 21% price difference, I get the same truly large-sized sensor fully functional "DV" camera, except for the power zoom! Whilst the shallow DoF for movie recording is amazing, I now do have a really usable full-time AF during movie recording with total silent operation of continuous focusing and moreover for the exposure control by real-time variable aperture as well, which is also completely silent. In fact, my RED NEX can be pretended to be a real RED camera, and practically it is far more usable than the Canon 5D MkII for most of the family causal movie shootings.
2. All other specs of the 3 and 5 are the same. I enjoy the same brilliant articulated high resolution LCD monitor with anti-reflection coating. I enjoy the 7 frames per second continuous shooting mode. I can use the same one-scan automatic stitching panorama mode. I can have the full time quick and continuous CDAF in movie mode. I have the same responsive and accurate face detection AF mode for taking still pictures.. and so on.
3. NEX-3 has four colours to choose, whilst the NEX-5 has only two. And, the silver colour of the NEX-3 does have a better match to the metal shiny silver kit lens, but the silver NEX-5's does look dull, on the contrary. Well, you know, as spoiled by Pentax in the recent years, I am a colour-hungry person for cameras! (I have bought the Silver *ist DS, my Olive K-m and then my Navy Blue K-x these years.)
4. NEX-3's on/off switch is at a more convenient position than the NEX-5 that can be easily turned by the thumb, i.e. concentric with the shutter button. And I prefer this "Pentax" style design as I have been adopted to it for long (since the MZ-S). ;-)
5. NEX-3 records videos in MP4, which is a format which has far better compatibility. Moreover, the AVCHD format and file structure (with multiple folders+sub-folders and files inside) is really troublesome, I have to say. Once the structure is destroyed, the videos cannot be played back at the camera.
6. NEX-3 has the 720p(/30fps), whilst NEX-5 only has the 1080i(/60fps) but no choice of 720p. If MP4 format is chosen at the NEX-5, it will give you a strange format of "1080p" at 30fps at a forced 16:9 aspect ratio but actually sub-sampled at 4:3. As such, many software players do not recognise and playback the video and its aspect ratio correctly. Last but not least, compressed 720p is easy to playback smoothly on more modern PC machines than the 1080 ones. What is the point of having "higher" resolution if one can't get a smooth *video* and playback?
Btw, do note that both MP4 and AVCHD videos are actually H.264 compressed. So, actually there should be no difference in image/video quality, against what Sony and Panasonic are claiming! Afterall, only the bit rate and compression ratio counts actually!
7. NEX-3 is slightly larger and thus is a little bit more balanced than the NEX-5, as it looks and feels.
8. The lack of an IR remote controller support is not a major issue for such a "P&S" camera, which does not support wired cable release anyway (at least by now), just like the K-x.
9. The shallower grip is not a real issue to me, as we used to have no grip for most P&S DCs, right? :-) On the other hand, the grip of the NEX-3 is broader, which would be more comfortable to hold for some people.
10. The non-metal body is a non-issue to me, as I have been used to have all those plastic DSLR bodies from Pentax, since the *ist D!! :-o (except the K-7~)