Well, like I said, it has to be done manually. Meaning I have to go through each category and number them one at a time.
What I usually do is number them by 100s instead of 1s. Meaning I display an entire category in my Admin CP (the most you can display is 200 at one time if I'm not mistaken), then I number them one at time by 100s. So, anything starting with A gets 100, anything with B gets 200, anything with C gets 300 and so and so forth. Use the TAB button to jump to each field, rather then selecting them with your mouse. This cuts the time it would ordinarily take to do this in half. When I'm done with a page I save it, then go though the next page (make sure the other smilies where already set at the same number or less then 100 before you even start).
Once you get all your smilies order by 100s then you can go back through and refine them now that their at least in some kind of alphabetical order, by setting all the ones that start with AA to 100, all the ABs to 101, all the ACs to 102. You get the idea.
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