We can follow the old wikis (ggFTW) guideline, I think it is pretty handy.
Which means that the filename should correspond exactly to the item's name. Example:
Item: Secret Card No. 5
Icon (the small image): Secret_Card_No._5.gif
Image (the big image) Secret Card_No._5.png
If we want several images of the same item, for example different views of a wing equipment, we can name it as: Something_2.png, Something_3.png and so on (but keep the first one as Something.png).
As for the skills icons being .jpg instead of .gif, I think we should re-save those images so they are .gif. Or else it may be difficult to predict the filename :o