We use PasDoc http://pasdoc.sourceforge.net/ for API documentation.
Michalis, an author of this engine, is also a PasDoc developer,
so suggestions about PasDoc improvements are also welcome :)

We use @section and @groupBegin / @groupEnd tags in our documentation,
although they are not yet implemented in PasDoc.
I plan to implement them one day, see
http://pasdoc.sipsolutions.net/MichalisKamburelis

We use PasDoc with --auto-abstract option. This is very handy,
and it forces us (in a "good way") to write really good 1st sentence
of every documentation comment. Do's and dont's:

 - Do not start a sentence with "This..", in particular "This function does
   the job of calculating the sensor." or "This returns the calculated sensor
   value." or "This causes sensor value to be calculated."
   or things like that. Usually, the clumsy "This..." part of the sentence
   can be simply removed. Your sentence should simply describe what the
   function / class etc. does, as shortly as possible.

   This problem comes usually from a need to use a verb in the 1st documentation
   sentence. Well, there's no need for it. If you have a function
   named "SensorValue" (although "Sensor" seems even better), then user
   already knows that the "sensor value" is calculated by this function.
   The documentation string can be just "Calculate the sensor value.",
   "The sensor value.", or simply nothing, as the function name already
   says everything.

 - Write the documentations like orders, not like description.
   E.g. "Do calculation.", not "Does calculation.".

 - Do not start the 1st (or, preferably, any other) sentence with
   the name of the item you're just documenting. If you document
   method FooBar, do not write "FooBar does something cool."
   or "FooBar is the collision tag.".
   User reading the description already knows the name of item,
   so just write "Do something cool." or "The collision tag.".

 - Using "I.e.", especially at the beginning of the sentence, looks
   clumsy and often should be removed, this forces the sentence to be simpler.
   If you *really* have to, start the sentence with "That is".

 - Do not write "Will be called...". Just "Called..." is OK.

 - *Always* make a unit description, for every unit. They are handy
   at PasDoc's unit list.

 - Often, we have a unit with only a single / a few classes.
   In such cases it's best to place most of the documentation at the class,
   not at the unit description --- since the class is the actual item being
   described.

   Unit's description should then contain a very short description of the class,
   in plural form, and a link to the class. Like
     { Scene manager (TKamSceneManager) and viewport (TKamViewport) classes. }
   or
    { OpenGL bitmap fonts (TGLBitmapFont). }

 - Do not start every documentation string with "Simple..." or "Trivial...".
   We have a lot of simple and trivial wrappers over something else,
   and it gets tiresome when every comments mentions this :)
