Which Mini-ITX case should i get?

Well you can rule out the Elite 110 straight off, as it only supports short graphics cards and yours is around 50mm too long. It's also probably a bit overpriced right now, it's fairly new so I'd assume it'll drop to Elite 120/130 levels soon. There are ways to get the stuff you want into a case this small, but it's probably not an optimal solution.
I'd also rule out the Elite 120. The Elite 130 is basically the same thing with a few minor revisions.

Cable management
None of them. Most ITX cases are near to non-existent in terms of cable management, though each one has it's own quirks. The Elite 120/130 really favour a modular/semi modular PSU to reduce the amount of cables hanging down, the 250D has the PSU at the bottom so isn't quite as bad in this regard. Either way, it's unlikely you'll have a very "clean" build with any of the options. I'd also be wary about "windowing" if it removes any vented sections (though you can always vent the window).

Cooling/airflow
None of the three cases have very good airflow, your best bet in that regard would be a Bitfenix Prodigy or Fractal Design Node 304, but they are perfectly serviceable if set up correctly. All three of the cases you mentioned are essentially built for closed loop cooler support (at least if you are overclocking) so a lot of your selection might be based on the type of CPU cooler you had in mind.
Quick version -
Air cooling - use an ASRock Z87E-ITX or Asus Z87-Pro in a Bitfenix Prodigy or Fractal Design Node 304. This gives you access to a large number of oversized air coolers as well as popular cheaper models like the Hyper 212.
H100i (or similar 240mm AIO) - use a Corsair 250D or Bitfenix Prodigy. If using the Corsair 250D, use a motherboard without connectors along the top edge of the board (such as the ASRock and Asus models) as these will block the cooler significantly.
H60 (or similar 120mm AIO) - use an Elite 130 for size/value (though most of the other cases can use these too). Motherboard is pretty flexible, the MSI you picked is great value.


About your build in general -
If you aren't bothered about overclocking, you can save a significant amount of money by going for a similar non-overclocking version (anything up to maybe £200) which can go into graphics or your pocket. Either way it's a win.
You shouldn't have any issues with the heatsinks on the memory, but conventional wisdom is to get slightly lower profile memory to avoid a potential problem in smaller cases.
650W is way more than you need, as it stands you could comfortably settle for a 500W. The 650W Supernova wouldn't be my first PSU choice, as it's OEM is average and the handle on the back might be annoying on a compact build, but it is very reasonably priced.