Hi Stefan,
I have tested this with Age of Myhology (Titans 1.03) on wine-1.1.7-106-g38815e1, patches 1-11 don't seem to cause any problems (haven't checked extensively though), but upon applying the 12th (0012-WineD3D-ARBvp-ffp-replacement.patch) the water lost it's transparency [1].
I'm not sure what other information you need, so just let me know. I'm happy to test any changes you make.
Chris.