Will the gog.com version of JA 2 work with stracciatella?
http://ja2.dragonriders.de/index.html
Thank you. :)

I would think so, since all you need apparently are the original data files, which should be there after you install the game via WIndows/Wine.
I'll certainly be using the Linux port.

Have you had any success? :)

Heh, I can't get the 0.10 snapshot to compile on Gentoo/GCC 4.3.
I'll try a SVN snapshot later on and see if they've fixed it.
But from the look of it, all the data files you need should be there in the GOG version after you install it under Windows or WINE, you can actually follow the instruction on the stracciatella site if you run Ubuntu or something.
EDIT: Ah, it was my 64 bit OS, not GCC 4.3.
Compiled it and tested with the default GOG JA2, seems to work just fine!

Is it better to use this or the unofficial patch for Windows with Wine?
http://ja2v113.pbwiki.com/

If you mean is it better to use stracciatella or wine and the 1.13 patch, it's up to you. The stracciatella port is meant to be somewhat vanilla, while the 1.13 patch is windows only and adds some enhancements like more resolutions and such.

1.13 works perfect with CrossOver Games (commercial Wine). :)

1.13 even runs better in Cedega (videos and gameplay are very smooth).
http://www.cedega.com
:)

A small addendum:
On my low leve machines (EEE 900A), the Stracciatella port runs significantly faster than Ja2 (1.12 or 1.13) under Wine. So I would recommend going the Stracciatella route if oyu have a similar machine.