The winners of our 2008 "Best-ter-est of Omaha" awards were Alvarados, El Aguila, Guaca Maya and La Mesa, but honestly, I think a lot of people (including myself) haven't fully explored the South Omaha area. Without doing so, I don't think one can declare a "Best Mexican Restaurant" in Omaha, only recommend what's been the best they've found so far.
With that said, I'll be updating this map with the places that I've tried, or have heard from trusted sources, that are some of the restaurants in Omaha to find truly great authentic Mexican cuisine (though I reserve the right to include any Latin American restaurants).
Map of the Best Mexican Cuisine in Omaha
I also encourage everyone to share your favorite spots. I'll use those recommendations as my TODO list when trying to decide where to eat next.