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It must be joke to ask for native look&feel for Linux. Putting aside things like Gnome vs KDE, and diffident distributions they are changing so dramatic now. I'm using Lunux for last 6-7 years everyday, and still I'm not able to use Gnome3 or Unity on Ubuntu - same window manager and same distribution I use science 5 years...
Soon Win8 will be probably so different form Win7 as Win7 is to WinXP.
Mac is probably more conservative, but still they are changing UI.
If people who make this "native" look&feels don't care why do you?
I think your UI should be so easy that my son, who use mostly iOS or Android, could also use your application on FreeBSD even if he see this OS for a first time in his life.
Who is your main user? Someone who spend last 10 years on front of the same computer? If not what is native for him - not for OS he just happen to use today.
Since "Linux" contains several environments and several GUIs I will make an interface for each environment (going as far as I can, since it will be nearly impossible to cover them all).
That's the reason for asking the community. Let me know how you think an "native" app should look in *your* environment (even if it's Blackbox, Haiku or something else) and I will keep it in mind when I create that particular interface.