You can replace the default IconSet for those places where a larger icon image appears in Yanfly's plugins ItemCore and ShopMenuCore
This allows you to use another IconSet in Yanfly Item Core and Shop Menu Core. Screenshots below.
Put this below Yanfly Item Core and/or Shop Menu Core plugins. Configure this plugin parameters. They are pretty self explainable:
Then write in the item / skill / weapon / armor notetag the icon's place in your new iconset.
If you don't write anything in the notetag it will load the default IconSet as it was by default.
Note: the first icon starts at row 0 and column 0.
<bicon row: x> <bicon column: y>
Setup of the item: http://puu.sh/lfIYZ/5d0acb0ddd.png
In game with the new IconSet: http://puu.sh/lfIFz/291ea2ad03.png
In game with the default IconSet (didn't setup this item so it goes back to the default): http://puu.sh/lfJ1k/33b2696782.png
In Shop: http://puu.sh/mDGjR/92422bc50a.jpg
With a weapon: http://puu.sh/mDGu5/7f84469a67.jpg
This uses Yanfly's Item Core plugin. Use his/her license. From my part, use at will
The icons in this example were taken from http://game-icons.net/ and they license them as Creative Commons v3. Read more here: http://game-icons.net/about.html
Hint: click the RAW button and save its contents.
Plugin: https://github.com/bsides/rpgmakermv/blob/master/BSD_OtherIconSet.js - save it as BSD_OtherIconSet.js
OtherIconSet example (1.78mb): https://github.com/bsides/rpgmakermv/blob/master/img/system/OtherIconSet.png
1.1: Now supports Yanfly's ShopMenuCore. Rows and columns traded places (was wrong before, sorry!).
PS - I don't know if this is the best way to write an extension, but I know it works. If you have any suggestion or criticism, please let me know.
Please, use the github tool to report bugs or any other comment. You may also post in this RPGMaker's forums: http://forums.rpgmakerweb.com/index.php?/topic/50732-other-iconset-for-yanflys-itemcore-and-shopmenucore/