This is the current list (26 September 2015) of All-Time-Downloades according to the eShop chart in my part of the world (Sweden).

Mario Maker is just about to enter at the top twenty list.

Downloadble retail games - - - - - - - - - - - - - - - - - - - - - - - -  Virtual Console

1. TLOZ:WW HD (free if you bought MK8)

2. Wii Street U (free in the beginning of the Wii U launch)

3. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -SMW

4. Trine 2 (one of the first downloadable games)

5. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -TLOZ:ALTTP

6. MK8

7. SM3DW

8. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Metroid Prime Trilogy

9. Ducktales Remastered

10. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -SMB3

11. Splatoon

12. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -SM64

13. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -SMG2

14. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Earthbound

15. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -TLOZ:Minish Cap

16. SSB for Wii U

17. Art Academy: Sketch Pad

18. NES: Remix

19. Hyrule Warriors 

20. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -SMB

* * * * * * * * * * * * * * * * The rest (without known order) * * * * * * * * * * * * * * * *

Shovel Knight- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TLOZ NES

Super Mario Maker- - - - - - - - - - - - - - - - - - - - - - - - - - - DK64

Rayman Legends- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Super Metroid

Child of Light- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - SMB2

MP10- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TLOZ: OOT

NES: Remix 2- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Mega Man 2

DKC:TF- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - DKC

NSMBU- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Super Mario Kart

Captain Toad- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Brain Training

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Mario & Luigi: Superstar Saga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Mega Man

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Zelda 2: TAOL

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Mega Man X

Possibly younger gamers who didn't have the old consoles and those who missed the Wii VC. And in Earthbound's case, it's actually the first time it got released in europe, so for us europeans it's basically a new game.

Japan

1. Splatoon ~91,399**

2. Dragon Quest X 

3. Pokemon Rumble U

4. Mario Kart 8

5. Art Academy

6. Super Mario Maker

7. NES Remix

8. Super Mario World

9. Super Smash Bros for Wii U ~43,522**

10. Brain Age 2

11. Super Mario 3D World

12. EarthBound

13. Pikmin 3

14. Kirby Super Star

15. New Super Mario Bros U

16. Nintendo Land

17. Super Mario Bros

18. Mario Galaxy 2

19. Xenoblade Chronicles X ~22,802

20. Pikmin Short Movies 

** = Digital Estimates minimum sales.

Do all regions release official information about eShop sales?

Yes, there should really be an official thread about this.

Here's the German list as of today:

1. Wii Street U
2. Wind Waker HD
3. Super Mario World
4. Trine 2
5. A Link to the Past
6. Super Mario 64
7. Art Academy: SketchPad
8. NES Remix
9. Metroid Prime Trilogy
10. Minish Cap
11. Super Mario Galaxy 2
12. Super Mario Bros. 3
13. DuckTales: Remastered
14. Splatoon
15. Dr. Kawashima
16. Mario Kart 8
17. Donkey Kong 64
18. Cube Life
19. Super Mario Kart
20. NES Remix 2

EDIT: Russia (UbiSoft games were really cheap at the end of last year, AC games for less than 5€ for example):

1. Wii Street U
2. Trine 2
3. Rayman Legends
4. DuckTales: Remastered
5. ZombiU
6. Super Mario 3D World
7. Mario Kart 8
8. Wind Waker HD
9. Art Academy: SketchPad
10. Super Mario Galaxy 2
11. Metroid Prime Trilogy
12. Child of Light
13. NES Remix
14. Rabbids Land
15. Captain Toad
16. Tropical Freeze
17. Assassin's Creed III
18. Toki Tori
19. Toki Tori 2+
20. SteamWorld Dig

South Africa:

1. Wind Waker HD
2. Wii Street U
3. Super Mario World
4. Trine 2
5. A Link to the Past
6. Mario Kart 8
7. Super Mario 3D World
8. Metroid Prime Trilogy
9. DuckTales: Remastered
10. Super Mario Bros. 3
11. Splatoon
12. Super Mario 64
13. Super Mario Galaxy 2
14. EarthBound
15. Minish Cap
16. Super Smash Bros. for Wii U
17. Art Academy: SketchPad
18. NES Remix
19. Hyrule Warriors
20. Super Mario Maker

Reserved

Well, guess I'll have a look. Not sure if it's just for Luxembourg or also for Belgium as we share a market on international level (Which can get really dumb at times for us in Luxembourg: For instance, I needed a belgian adress for the Club Nintendo, which I couldn't provide, limiting me to digital goods).

Good to see Metroid Prime Trilogy so high.
And yes, an eShop thread with monthly updates or something would be great!

How did you get the lists from Russia and South Africa? Trough friends or did you create another account?

Wasn't Wind Waker HD initially released exclusively through the eShop? That would explain why it's at the top of many eShop lists (in addition to the MK8 deal, of course). For reference, here's the Top 20 for the US (not sure if this includes all of NA):

1. The Legend of Zelda: Wind Waker HD
2. Super Mario World
3. Wii Street U
4. Super Metroid
5. EarthBound
6. Pikmin 3
7. Super Mario Bros. 3
8. Super Mario Bros.
9. New Super Mario Bros. U
10. Mario Kart 8
11. Punch-Out!! Featuring Mr. Dream
12. Metroid Prime: Trilogy
13. Super Mario 64
14. NES Remix
15. Splatoon
16. Super Mario Bros. 2 (>132k)
17. The Legend of Zelda
18. Kirby's Adventure
19. Super Smash Bros. for Wii U
20. The Legend of Zelda: A Link to the Past