There are no standards unless you are developing for specific hardware (really only if were talking very old hardware) or engine.

If you want it to be widely useful that the best bet is to keep it as simple and easy to use as feasible.

For example a platformer could have one in front of sprites foreground layer, one behind sprites forground layer plus an optional parallax background layer which should be sufficient for most cases. This would allow for grass drawn infront of a character's feet and a ladder drawn behind the character.

1. On really old machines with hardware support for tiled graphics, you're restricted to the number of layers that hardware was designed to handle.

   For modern hardware there is no strict limit on the number of layers one can have. Your only real limit is how many pixels you can shovel per frame.

   Without hardware limiting things, there are several reasons for wanting to put a limit on the number of layers:

   • Simplify level design. You don't have to worry too much as to which layer(s) you should be painting tiles into as the choices would be obvious.
   • Puts a maximum limit on the number of tiles rendered per frame. This would allow you to compute the maximum render times and infer performance requirements and minimum specs. If a large number of layers are allowed, one can put together complex scenes with a small number of tiles piled upon each other but this can result in a severe performance hit when that part of the level is on screen.
2. Semi-transparency is okay, although it does depend a bit on how and where it's used.
   • For objects that are normally transparent, it is generally okay. Such as glass windows or holo-displays.
   • Shadows. A semi-transparent black layer is an easy way to add shadows to arbitrary tiles.
   • Darkening/tinting. This can work, but it does carry the performance hit of need to render the affected tiles twice (once for the normal tile and once for the darkening version).
3. Rotation and mirroring can work on tiles, although it does require support in the engine being used. You also have to keep in mind any lighting that's baked into the tile will probably look wrong after rotation or flipping.
4. Being generally useful depends on how similar it is with other tilesets and how much massaging is required to make them work nicely with each other. You might want to browse some of the platformer sets on this site and consider how well they fit together (or don't).

1. I typically use a background layer for tiles which I use for the floor/ground.  Then I have a decorations layer to decorate the ground/floor with small details, like bullet holes or long grass.  Then I combine those layers in some cases (not always) to improve performance.  Basically, you use whatever you need and just try not to overdo it.  If the commissioner wants to limit the layer count, that should be made known to you before the work is done.

2. a. Semi-transparent tiles are very uncommon.  If you want to have dim versions of tiles, you typically modify them using tints or color manipulation at runtime.  It doesn't really hinder performance much.

2. b. Rotating/flipping tiles should be expected to be done by the end user or developer in most scenarios.  Some exceptions should be considered, like ground tiles for each corner and side.  The reason you pre-flip and pre-rotate these tiles is you may want to change a few pixels for some added variety and such tiles are typically already set up a certain way in tile sets.  Just use your best judgment.

1. Engine I use in my RPG has four layers for map objects: Floor/Wall, Objects, Decoration and Top.

Plus there can items, effects and character layers but four for map objects. Floor/Wall layer is pretty self-explained. Object layer could for example window tile and decoration might be curtains. Then Top layer is reserved if object immediately below is tall for example tall floor lamp.

You should also think if it makes sense to have plain curtains without window. It might make sense if you have multiple windows and curtains which then could be mixed in the game. I am using curtains example here.

2. I think making darker or lighter version is not needed since lighting effects should be done by the game engine. Rotating/flipping tiles could be done before hand especially if there is added some variety or some tile is not mirrorable. For example character might have scabbard.