Recently playing with my N9 and my girlfriend's one I've noticed some differences in how two of them operate. These are very subtle ones / like how fast the screen rotates when changing from vertical to horizontal, how light sensor reacts to the bright light or that one has more greenish tint to the screen while the other have more reddish one. They're both the same - black, 16 Gb, bought in the same shop and running PR 1.2. However, I've checked exact firmware that they have and it differs - I flashed mine by hand with navifirm - and it corresponds exactly to the model and country (16Ggb Switzerland, black) I have, while my gf just updated when the PR 1.2 came out - and her firmware corresponds to 64 Gb N9 (also Switzerland, also black). And here come my questions:
1. Why the automatic update brought 64 Gb software to a 16 Gb N9?
2. Did anyone tested various firmwares to check if some are better/worse than others?

I'm fairly sure that the firmware doesn't truly matter, whether it's the 16gb or the 64gb version. I could be wrong though, so please feel free to correct me. I'm just saying that because the storage capacity is literally the only difference between the two.

I haven't had my N9 since it was released. When I got mine, it already had PR 1.1, then I upgraded to PR 1.2. From my experience, PR 1.2 is much better than PR 1.1. Everything seems faster and smoother. Of course, PR 1.2 isn't perfect, and my only complaint is the small stuttering you get when using the default video player. It's extremely subtle, but it is there. That much I'm sure of.

i have checked if some fw scores better on html5test than other, and morw fluid,

Great - could you share what was the result?

My friend got his n9 from singapore and scores 284 on html5test, and i dont know, for me its more lagging than mine, and here is my resulthttp://db.tt/FJvWVakI

mine is cyan 16gb(indonesia) and my friend has 64gb from singapore, and we are both on PR1.2

If you have a 64GB phone, chances are that it will get slower and lag a bit when you start loading it up with many apps and files and stuff. So perhaps the 64GB firmware is tweaked just a little bit to accomodate for these lags, while this is not required in the 16GB version. So maybe installing the 64GB FW on the 16GB one can make it marginally faster? I dunno, I'm just throwing ideas here.

vanilla firmware flash for 16GB and 64GB is the same file, so there is no difference on for example on default 001.bin as the same file is used for both hardware versions.

Only difference starts to happen if you flash operator or country variants, as in there there can be some operator/country specific tweaks around.

I was playing with both N9's some more and I've noticed other differences: one detects noticeably lower wifi signal (or at least that is being shown by the software) than the other.
I doubt that this is hardware related, as they're both made in Finland - firmware again?
I think when I get some spare time I will try to flash different firmwares (country-wise and memory-wise) to check their performance in everyday use. Therefore, one question:
is it possible to backup applications? I mean, I've used Nokia Link to to a backup but in the end, I was informed that apps I had on the phone were installed through Ovi Store and that I have to restore them manually. Is there any other way?

Currently there is no public way. I might be releasing my backup application for coding competition (which also has ovi store applications downloader&reinstallation functionality), but I haven't yet decided if I will release my application to public or should I just keep it private.

PS. and its a bad idea to try to flash different variants, since then you cannot downgrade back to vanilla variant anymore.

Oh, I was not aware of that - could you explain why?
And as for your backup application - I think you should definitely release it - sharing is caring, right?