Setting aside DSLR bodies (limited MF aids, potential register distance issues with legacy lenses & size/weight), you are looking at 4 main mirrorless camera systems
- Micro 4/3's (m43). 2X crop factor, supported by both Olympus and Panasonic
- Sony APS-C NEX (1.5X crop factor)
- Fuji X-series - APS-C
- Sony A7/A7r full frame - very new and likely out of your price range
Disclosure of I am a Fuji and Olympus m43 user - I have very limited experience with the NEX. Some observations in no particular order
The Fuji system has, IMHO, the best image quality of the mirrorless cameras except for the new A7. It also has the highest quality native AF lenses. It is a rangefinder style body (but not an actual rangefinder) that is pretty retro in that it has actual knobs/dials for most basic exposure controls (including an aperture ring on the lenses). They have focus peaking and a simulated split image rangefinder, although the latter feature is not that impressive to my eye.
The recent m43 bodies (anything with a 16MP sensor in it) have the fastest AF performance (by a fair amount), the Olympus bodies have in-body image stabilization (IBIS), there is a pretty extensive selection of lenses available (many of which are quite good) and the cameras tend to have all the latest geeky bells and whistles. The only MF aid is magnification unless you get a recent body such as E-M1, E-P5 or GX7.
The NEX cameras are a little quirky (they drive more like a computer than a camera to me) and their native lens selection (AF) is rather pedestrian. They are said to have a particularly effective focus peaking implementation, but I have not compared it to the Fuji. While being APS-C, the IQ is really not any better than the current generation m43. The NEX 7 is 24MP but at the expense of noise.
Without knowing what "low cost" means to you, a Fuji X-E1 kit with the 18-55/2.8-4.0 lens (which is a really great zoom) either new or refurbed is a great value right now. The X-E2 just came out (and it is a better camera) and X-E1 prices are low. The X-E1 EVF is nice, but suffers from a significant refresh rate drop off as light levels go down. The rear LCD is OK but nothing spectacular. The X-E2 fixed both issues along with faster AF. The Fuji lenses are exceptional, although not inexpensive. One nice trick on the X-E1/X-E2 is that the pop-up flash can by held by a finger on your left hand to point upwards for bounce work. Not much power, but it comes in handy.
The E-M5 is another great bargain either refurbed or used. It offers a spectacularly effective IBIS system, a very good EVF, but no focus peaking at all - this might be a concern if you plan on extensive use of legacy lenses. It does not have a pop-up flash although it comes with a small hotshoe unit that is powered by the body.
I've never gotten on too well with the NEX cameras, so I'm not much more help there.
I'll say that I absolutely love my Fuji X-E2. I have been shooting for almost 40 years and currently use Olympus m43, Nikon D800 and the Fuji. The Fuji is by far my favorite camera to actually use and carry. There are a number of Fuji X users here on RPF for help, too.
