Japan sales - Media Create, Famitsu, Dengeki: week 39 ( Sept 23 - Sept. 29 )

[retroking1981]

Kresnik said:

[N64] The Legend of Zelda: Ocarina of Time (Nintendo) {1998.11.21} - 386.234 / 1.147.068
[NDS] The Legend of Zelda: Spirit Tracks (Nintendo) {2009.12.23} - 320.940 / 740.109
[N64] The Legend of Zelda: Majora's Mask (Nintendo) {2000.04.27} - 314.044 / 601.539
[NDS] The Legend of Zelda: Phantom Hourglass (Nintendo) {2007.06.23} - 288.282 / 902.386
[GCN] The Legend of Zelda: The Wind Waker (Nintendo) {2002.12.13} - 287.346 / 742.609
[WII] The Legend of Zelda: Skyward Sword (Nintendo) {2011.11.23} - 194.894 / 337.452
[NGB] The Legend of Zelda: Oracle of Ages (Nintendo) {2001.02.27} - 191.802 / 373.361
[NGB] The Legend of Zelda: Oracle of Seasons (Nintendo) {2001.02.27} - 190.029 / 372.693
[3DS] The Legend of Zelda: Ocarina of Time 3D (Nintendo) {2011.06.16} - 182.998 / 586.505
[WII] The Legend of Zelda: Twilight Princess (Nintendo) {2006.12.02} - 145.068 / 554.109
[GBA] The Legend of Zelda: Minish Cap (Nintendo) {2004.11.04} - 92.882 / 235.400
[GBA] The Legend of Zelda: A Link to the Past + Four Swords (Nintendo) {2003.03.14} - 84.107 / 293.989
[GCN] The Legend of Zelda: Four Swords (Nintendo) {2004.03.18} - 54.782 / 127.399
[NGB] The Legend of Zelda: Link's Awakening DX (Nintendo) {1998.12.12} - 49.513 / 314.224
[GBA] Famicom Mini: The Legend of Zelda (Nintendo) {2004.02.14} - 36.861 / 217.901
[GBA] Famicom Mini: Zelda II - The Adventure of Link (Nintendo) {2004.08.10} - 35.335 / 141.826
[WIU] The Legend of Zelda: The Wind Waker HD (Nintendo) {2013.09.26} - 31.154 / NEW

Looking at re-releases only WWHD's sales (whilst admittingly bad) are more in line with what you'd expect. The other re-releases were all on much more popular HW and OoT3D which is way out in front is a re-release of the most popular game*.

*I'm aware the NES ones sold more but the re-releases of those had nothing added/improved and were very outdated at the time.