Hands down, my best friend in the fight against my wife's headaches has been shallots. We learned very early on that onions are a trigger for her. Most tasty foods require onions, so a substitute was absolutely necessary if we were ever to enjoy delicious food again.
Shallots present some challenges. The most obvious place to buy them is in the local chain grocery store. However, they are difficult to find. They come in very small and EXPENSIVE bags. When we began the diet, we were facing some financial pressures and were pinching every penny. The shallots in these bags tend to be disappointingly small, which means more work and less food per ounce.
We found two alternatives to tiny shallots in tiny bags with huge prices: first, we discovered that shallots can be found in bulk, or in giant bags, at our local farmer's market. The prices are ridiculously cheap in comparison to retail grocery stores. The shallots at the farmer's market are much larger, as well. They tend to be better quality, though that is not always the case. Avoiding giant bags in favor of hand selecting from the bin solves this problem - look for shallots without the large dark or dry spots. As in most cases, avoid organic if you want to save the most money.
We also found that shallots are available at the local Mexican markets in bulk. They tend to be smaller, and are not as good as the best ones at the farmer's market. However, they are good and cheap enough that a special trip for this purpose may be worthwhile.
Preparation is similar to onions, even down to the tears. The best way to deal with them is to get a library book on knife techniques, or watch a video on YouTube. Cooking shallots like a chef helps make the process efficient, the tears rare, and the pieces uniform for even cooking.
Shallots have certain advantages and disadvantages over onions. Shallots do not have the same taste as onions; they are considerably milder. I miss onions terribly and eat them out whenever I can. Shallots are a tolerable alternative, but not a perfect one. On the other hand, shallots are milder than onions and make a nice raw ingredient in salads, salsas, and other dishes.
Ultimately, the advantages of shallots greatly outweigh their disadvantages. So many styles of cooking depend on onions as a key ingredient and shallots provide a perfectly reasonable substitute. With shallots, the migraine cook can explore every form of cuisine from Cajun to Cuban, French to Italian, and Mexican to classic American. Make your peace with shallots and they will become your best friend in the kitchen.