I found the menu but it doesn't work.
When I assign "wine /opt/path/to/program" to this file and when I want to open this file by double click then, nothing happens. Not even the pressor load rises, so my guess it, that Gnome still doesn't know what it has to do with this file.
When I look back into the menu, wine seems to be assigned for these files but obviously Gnome even doesn't know it.

What did you put in the custom command box exactly? It works perfect here.

When I use a "real" program like acroread, Gnome saves my decission and a double click on PDF-files works the next time.
When I use wine with a parameter as path, I have the following problem:

I right click the program file of this program I use with wine -> Properties -> Open with -> ADD (I fill out "wine /opt/program/program.exe")
When I leave the menu and go back to nautilus and want to double click this file again, nothing happens.
I choose open with and already find a "wine"-entry a lot of times due to my last tries to get this to work although I deleted all the wine entries from the properties menu.
I choose any of these wine entries and the program starts.
When I try a double click on the file next time, it doesn't work again. Nothing happens. That means that Gnome knows, what this wine entry means,
because I'm able to choose it from the given menu from "open with", but I cannot open it with a double click.
Again, it only doesn't work exactly in this case with wine. With other files it doesn't seem to be a problem, because after the update to Gnome 2.24,
Nautilus wanted to open PDFs with Gimp?! I don't know how this weird behaviour appeared, but switching to acroread worked perfectly and from this time on, I was able to open PDFs with a double click.

When I put notepad.exe in my /home, and assign "wine /home/jan/notepad.exe" to text files, it opens fine. I added the command without the quotes.

This works here too.
It even works when I click text files and want to open it with notepad.exe. They open with notepad without problems.
But when I click ERwin files and want to open it with "wine /opt/Erwin/erwinerx.exe", they don't open. But it worked perfectly before I updated Gnome so something must be wrong here.
I surely didn't change anything in the program. So what could be the problem? I already delete all the properties entries and typed in wine /opt/Erwin/erwinerx.exe from new, but always the same problem.

What happens when you open a terminal and use:
wine /opt/Erwin/erwinerx.exe "/path/to/ERwinfile"

Does it start then, or does it give errors?

This works without problems.

Is this still an issue with gnome 2.26?

Yes, the problem still exists. Doubleclick on the "erwin files" doesn't do anything.
When I use the file command on the erwin file, I get the following:

$ file FILE.ER1
FILE.ER1: data

In Gnome, in the column type, it shows that the file type is unknown.

Btw: The System->Info about GNOME dialog still doesn't work yet.

The about gnome dialog needs gnome-python, this is in optdepends for gnome-desktop. I refuse to add it as hard dependency because I don't like to pull in gnome-python for a package which main feature is a library used by other applications.

As for your erwin files, I think nautilus tries to associate by MIME type, not by extension. the Erwin files don't have a known mimetype, I think nautilus has problems binding applications to it.

Thanks. You were right with the gnome dialog.
Should I write another bug report for nautilus?

I don't think that makes any sense, as the way gio and nautilus works is by using mime types. You might want to have a look at the shared-mime-info package and try to write a definition for erwin files though.