Ive always done it with similarity to the way CS_TBL suggested: However I either produce an overlay sprite layer where each tile has a range of more data than the tiles in other layers, but most of them being blank in the file (by storing the distance to the next sprite tile after each sprite tile, or just storing coordinates), or allow each tile to have a value that dictates wether they have 'extra' parameters that will allow much more storage information such as additional tile animimage, frame width/height speed etc.
Tile Animation
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