Oh, I knew about most of the ones mentioned by @credits , but didn’t knew there were cards from the same ‘set’ with copyright dates from 2003, 2004, 2005, AND 2006. TIL, thanks @credits ! 
Well, most has already been said, so not much to add (EDIT: not much to add, and here I ended up with this wall of text and pictures, rofl). The checklist provided by @dizzylochs is originally compiled by @tonysandlin and can be found in this thread. A great source which I use as well when making my Pokemon specific lists.
Three minor non-English things to add perhaps:
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The ‘English’ Energy cards without border and logo from the Theme Decks can be found in both the English theme decks and German sets. Although all other Energy cards in German are spelled ‘Energie’, this isn’t the case for the Energy cards from these EX era sets, which are spelled as ‘Energy’ and are a.f.a.i.k. identical to the English cards. Also note that all French, German, Italian, etc. versions of the EX era sets will be without the bar, unlike the English sets. The ‘Energy’ cards from the German set which are identical to the English theme deck cards can just be pulled from the set packs. (A.f.a.i.k. - not 100% sure about this one, since I’ve never seen any prove pack opening videos of German packs. I do know this set is released in German, and the Energy cards I’ve received from sellers which had it listed as German were all with ‘Energy’.
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English Uncommon cards from the EX Emerald set only have a single non-Holo code in Eric’s spreadsheet. But for whatever reason the foreign releases has two codes for the Uncommons instead of one, where the second code is identical to the code of the Reverse Holo versions. I for example included the Battle Frontier trainer card in my Seviper collection (since it contains a Seviper in its artwork), and for German, French, Italian, and Portuguese I have both the codes 2SC-NZB-1E1 and 2SC-NZB-IJA for the non-Holo card, but for the English I’ve only been able to find the code 2SC-NZB-1E1 for non-Holo (I’ve checked over 150 copies of this card in English, and none had the code ending in -IJA).
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In English, the Commons usually have three different codes; Uncommons one or two depending on the set; and Energy cards usually two as well. The same applies to European foreign releases (German, French, Italian, Spanish, Portuguese). The Japanese sets however, contain four different codes for Commons (both in 1st and unlimited edition; so eight unique versions for a non-Holo Common card from the set actually). Uncommons and Energy cards I’m not sure, but both will have at least two codes.
The codes of promo cards, Reverse Holo cards, Rares, Holofoil Rares, stamped cards, etc. will all be the same for the specific card. I don’t know any example where there are multiple different codes available for let’s say a promo card of the EX era. So in terms of codes you’ll only have to worry about set released non-Holo Commons, Uncommons, and Energy cards (see Eric’s spreadsheet for the English releases - unfortunately there isn’t a comparable spreadsheet for Japanese sets).
And to clarify some of the cards mentioned earlier by @aquaz and @mikejofthecoast with some pictures:
Kyogre/Groudon ex:
Original holofoil versions (given to participants of the Pokémon Ruby & Sapphire Challenge in the US in August 2003):
Regular non-Holo versions (inserts in the Nintendo Power magazine of October 2003):
Rare no bar non-Holo versions (inserts in the Australian K-Zone kids magazine):
EX FireRed LeafGreen Articuno, Zapdos, Moltres:
Regular Shattered Glass Holofoil versions (part of the set):
Non-Shattered Holofoil version (error - I only have a picture of an Articuno (as well as a second miscut one here)):
Non-Holo EX Delta Species Dratini and Larvitar with set stamp:
The non-Holo common versions are available with three different non-Holo codes, as well as a Reverse Holo in the set.
The non-Holo versions with stamp were inserts in the Swedish/Danish Donald Duck Magazine #49 of December 6, 2005:
A non-Holo version of the 035 Nintendo promo Pikachu was also available in the Swedish magazine Pokémon Official Magazine Summer Special, released in 2007:
https://instagram.com/p/BRGt129DSZ2
And there are probably more variations I’ve missed tbh. Not to mention all kind of language exclusive variations. 
Greetz,
Quuador
**Above - ENERGY SEACH - Thin boarder (c)2004 / Thick boarder (c)2003 with two different serial codes / Reverse holo
Jk. But i now need to reconsider what I’m actually going to do as far as editing my “collecting goal” and I need to rearrange my binders. Thank you again!