Gwyddion module functions remember parameters values between invocations and also between individual sessions. The place where all the values are stored is called settings. The settings include a few program-wide parameters as well.

The permanent storage for the settings is the file settings in a user's directory, this usually means under ~/.gwyddion (Unix) or Documents and Settings\gwyddion (MS Windows). The file is only read when Gwyddion starts and written when it terminates. You should keep this in mind if you want to do some manual modifications. Unknown entries in the settings are ignored but preserved.

The settings file starts with a magic header line

Gwyddion Settings 1.0

followed by lines with individual parameters and values (that form, technically, a serialised GwyContainer). Gwyddion writes the entries in the alphabetical order but this is not a requirement and you do not have to keep the order when modifying the file.

Each parameter line has the form

"key" type value

Typical module settings keys start with /module/modulename, although in a few cases the module name part is not actually the module name, either because several modules share settings or for historical reasons. Program-wide setting keys start with /app/. All possible value types are listed in the following table.

boolean Logical value that can be either True or False.
char Single character. Normal characters are represented directly using a single character. Special characters are represented using the hexadecimal notation as 0xXX. This parameter type is not actually used much by modules.
int32 Signed 32bit integer. Gwyddion writes them in decimal notation but reads also other notations such as hexadecimal.
int64 Signed 64bit integer. Gwyddion writes them in decimal notation but reads also other notations such as hexadecimal.
double Floating point number. They can be in the scientific format, e.g. 1.23e-4. They are represented in the standard C/POSIX locale, i.e. decimal dot is used (not comma or other separators).
string String of characters in double quotes, generally UTF-8 encoded. Special characters, including contained double quotes, are escaped using the standard backslash notation.

Some potentially useful program-wide options that can be modified by editing the settings file:

/app/restore-tool-positionboolean If set to True, Gwyddion restores not only size of tool dialogs but also their positions (if possible). For well-behaved window managers this is more likely to be annoying than helpful but in MS Windows you might want to try enabling it.
/app/3d/axes/disableboolean If set to True, axis labels will never be drawn on OpenGL 3D views, even if enabled. This can help with certain troublesome 3D driver/card/GtkGLExt combinations in which Gwyddion is likely to crash when it tries to draw the axes.
/app/help/user-guide-basestring Base location of the user guide for help. If not set, the default on-line location is used, i.e. something like "", depending on the language. If you want to use a local copy of the HTML guide, set this setting to directory name, for instance "/home/yeti/docs/gwyddion-user-guide-xhtml-en-2014-09-17".