CREATE_SUBDIRS helps a lot if browsing HTML documentation in a file browser.

ALWAYS_DETAILED_SEC makes sure everything has at least the automatic
documentation like function prototype and source references.

STRIP_FROM_PATH allows you to include only the relevant portions of the files'
paths, cleaning up both the file list and directory tree, though you need to
change the path listed here to match wherever you put SDL.

ALIASES avoids some warnings generated by
C:\source\svn.libsdl.org\trunk\SDL\src\joystick\darwin\10.3.9-FIX\IOHIDLib.h.
It seems Apple uses a few commands which are not normally supported by Doxygen.

BUILTIN_STL_SUPPORT adds support for parsing code which makes use of the
standard template library.  There isn't a lot of C++ in SDL (some in bwindow at
least), but this still seems like a good idea.

TYPEDEF_HIDES_STRUCT means that for code like this:
typedef struct A {int B;} C;
C is documented as a structure containing B instead of a typedef mapped to A.

EXTRACT_ALL, EXTRACT_PRIVATE, EXTRACT_STATIC, EXTRACT_LOCAL_METHODS,
EXTRACT_ANON_NSPACES and INTERNAL_DOCS make sure that _everything_ is
documented.

CASE_SENSE_NAMES = NO avoids potential conflicts when building documentation on
case insensitive file systems like NTFS and FAT32.

WARN_NO_PARAMDOC lets you know when you have documented some, but not all, of
the parameters of a function.  This is useful when you're working on adding
such documentation since it makes partially documented functions easier to
spot.

WARN_LOGFILE writes warnings to a seperate file instead of mixing them in with
stdout.  When not running in quiet mode, these warnings can be hard to spot
without this flag.

I added *.h.in and *.h.default to FILE_PATTERNS to generate documentation for
config.h.in and config.h.default.

RECURSIVE tells doxygen to look not only in the input directory, but also in
subfolders.

EXCLUDE avoids documenting things like test programs, examples and templates
which need to be documented separately.

I've used EXCLUDE_PATTERNS to exclude non-source subdirectories that often find
their way into source folders (such as obj or .svn).

EXAMPLE_PATH lists directories doxygen will search to find included example
code.  So far, SDL doesn't really use this feature, but I've listed some likely
locations.

SOURCE_BROWSER adds syntax highlighted source code to the HTML output.
USE_HTAGS is nice, but not available on Windows.

INLINE_SOURCES adds the body of a function to it's documentation so you can
quickly see exactly what it does.

ALPHABETICAL_INDEX generates an alphabetical list of all structures, functions,
etc., which makes it much easier to find what you're looking for.

IGNORE_PREFIX skips the SDL_ prefix when deciding which index page to place an
item on so you don't have everything show up under "S".

HTML_DYNAMIC_SECTIONS hides the includes/included by diagrams by default and
adds JavaScript to allow the user to show and hide them by clicking a link.

ENUM_VALUES_PER_LINE = 1 makes enums easier to read by placing each value on
it's own line.

GENERATE_TREEVIEW produces a two frame index page with a navigation tree on the
left.

I have LaTeX and man pages turned off to speed up doxygen, you may want to turn
them back on yourself.

I added _WIN32=1 to PREDEFINED to cause SDL to output documentation related to
Win32 builds of SDL.  Normally, doxygen gets confused since there are multiple
definitions for various structures and formats that vary by platform.  Without
this doxygen can produce broken documentation or, if you're lucky, output
documentation only for the dummy drivers, which isn't very useful.  You need to
pick a platform.

GENERATE_TAGFILE produces a file which can be used to link other doxygen
documentation to the SDL documentation.

CLASS_DIAGRAMS turns on class diagrams even when dot is not available.

HAVE_DOT tells doxygen to try to use dot to generate diagrams.

TEMPLATE_RELATIONS and INCLUDE_GRAPH add additional diagrams to the
documentation.

DOT_MULTI_TARGETS speeds up dot.

OUTPUT_DIRECTORY, INPUT and other paths reflect the fact that this Doxyfile is
intended to process src as well as include and is being run from a separate
subdirectory.  Doxygen produces several temporary files while it's running and
if interrupted, can leave those files behind.  It's easier to clean up if there
aren't a hundred or so files in the same folder.  I typically run doxygen in
SDL/doxy and set the output directory to '.'.  Since doxygen puts it's output
in subfolders by type, this keeps things pretty well organised.  You could use
'../doc' instead and get the same results.