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In which text file store Wine the settings. I wish to edit the Windows Version of Applications there.

It's in the registry and you'd better not edit it directly.
Now what do you mean by "Windows Version of Applications"?

Sounds like he means Wine Configuration. The applications tab allows you to change values to the installed libraries and the General tab allows you to change the Windows version.

Not sure why you would want to do it anywhere else...

To edit the registry, always use regedit.exe. It can be used interactively, but also from command line, so update can be scripted.
Structure of Wine registry keys are documented in http://wiki.winehq.org/UsefulRegistryKeys.
You want to create a value "Version" of type string into [HKEY_CURRENT_USER\\Software\\Wine\\AppDefault\\myapp.exe], this can be scripted as

cat << EOFINI > "$POL_USER_ROOT/tmp/windowsversion4app.reg"
[HKEY_CURRENT_USER\\Software\\Wine\\AppDefaults\\myapp.exe]
"Version"="win95"
EOFINI
POL_Wine regedit.exe "$POL_USER_ROOT/tmp/windowsversion4app.reg"
rm "$POL_USER_ROOT/tmp/windowsversion4app.reg"

(or whatever other valid version string)
With a recent version of PlayOnLinux that can also be done with

POL_Wine_UpdateRegistryWinePair 'AppDefaults\\myapp.exe' 'Version' "win95"

But that's undocumented, so I'm not sure it can be considered part of the stable API.

Edited by petch

Awesome! Nice tips Petch... Thanks!

Thanks realy lot for this.

I checked the "http://wiki.winehq.org/UsefulRegistryKeys" Website.
But could not found how to create driveletters. Is ther also way like the windowsversion one for that?

As in network drives or CD-ROM/DVD drives?

You can easily create drives to anywhere with Wine Configuration.
Just click the Drives tab
Click add
Select drive letter
Then browse to the path you want to use

Works with any folder or any CD-ROM... not sure if it works with networks?

I know the way over Wine Configurations. I hope I could get a faster way to add driveletters in Wine. At moment I have a batch file who set som settings like the exe files for specific Windows versions. Could maybe nice if i get the ability to set the driveletters also this way.

I'm sure there is a way, but it will take some "picking" the minds of the devs

Create symlinks into $WINEPREFIX/dosdevices/ subdirectory
http://www.winehq.org/docs/wineusr-guide/config-wine-main#AEN737