using vanilla kernel from distro or kernel.org

hi

I can find several kernels which are said to be compatible with my mini6410
board and i should use them. one is on the accompanied disk, the other from
"http://code.google.com/p/mini6410-debian/"; . but i was just wondering
except kernel configuration, is it any different to use the kernel from
friendlyarm or other kernels on the net than the vanilla kernel from
kernel.org or kernel source which comes with my distro (debian stable)?
are there any custom developments that have been done on these kernels,
which are not part of mainstream kernel?

Yes, and I talking more from mini2440 experience, there is quite a bit of
difference.  That is mainly in the hardware support area, commonly called
BSP (board support).  Some the changes live in the kernel source at
/arch/arm/your_machine (mach-s3c2440, for the mini2440) and a heap of patch
files.

You can try using the mainstream kernel and patching it. Finding patches
and writing your own for all the bits of hardware on your machine will be
big task.

Choices . . . get really familiar with the kernels supplied that you
mentioned and when something doesn't work try to fix it or find the fix. 
Another maintained kernel is found at Pengutronix.  There are things, which
at this stage do not work for the mini6410, but there is a community and
the support is good.  Everything for the mini2440 seems to work with their
BSP.

To get some idea of the work that goes into maintaining the kernel for a
specific board, go to :
http://www.oselas.org/oselas/bsp/pengutronix/mini2440_bsp_en.html
and  download 
OSELAS.BSP-Pengutronix-Mini2440-2012.02.0.tgz
extract it and look in
/config/platform-friendlyarm-mini2440/patches/linux-3.1 there are 27 of
them.  Have a look at what is involved in some of them.  Most are the work
of one person, but there are a few that are the collected wisdom of the
wider Linux community.

Then, more of interest to you, look at their mini6410 BSP.

Good luck!

thanks very much for clarification.