Black lines are caused by scaling to a non-integer internal resolution (anything other than Yx Native), texture filtering (Try anything that isn't bilinear (Forced), improperly offset textures (TC Offset, Wild Arms Offset hacks, Half-Pixel Offset), or improperly handled texture edges (Merge Sprite hack, Sprite/Round Sprite combobox). The native resolution, for the most part, fixes these issues. However, software rendering may be required as well.