Most people ask for bulkhead seating, and most airlines automatically offer bulkhead seating, assuming that the extra leg room will make the animal more comfortable. This isn't always the case. For those animals able to fit at least partly in the under seat storage, there may actually be more room in a regular seat. There may be additional under seat storage in the last seat on the plane, but be aware that close to the engines it will be noisy and may make some service animals uncomfortable.
Once you know what type of aircraft you will be flying check with Seat Guru for insider tips on which seats are the best. Remember that service animals are not allowed in exit rows, which, unfortunately, are usually the rows with the most leg room.