Most vendors do not publish their makernote specifications. Most of the specifications available on the Internet were reverse-engineered. Judging from the size of many makernote fields, manufacturers store a lot of information there and from the available specifications, some of this is certainly quite interesting. For example, makernotes may contain information about the lens used, contrast, saturation and sharpness settings, image quality settings, etc. For some more advanced camera settings, the Exif standard doesn't define a standard tag, so camera vendors have to resort to using the makernote. Unfortunately, in some cases, camera vendors store important information only in proprietary makernote fields, instead of using available Exif standard tags. The most infamous example for this is Nikon's ISO settings tag.

Most vendors write the makernote in TIFF format, i.e., in the same format as the rest of the Exif information is encoded. This appears to be a sensible thing at first glance. Unfortunately, in general it means that any change of an Exif tag, which moves the makernote field, will corrupt it. It is an inherent problem of the TIFF format that a writer must know the format and all extensions used, in order to be able to write changes correctly; unknown tags are potentially corrupted when they are moved (rearranged). But since makernotes are usually proprietary, Exif writers often don't know these details. The reason to write to the Exif data could be as simple as to add copyright information, an Exif comment, etc. Some camera manufacturers seem to have recognized this problem and now use a modified TIFF format with offsets relative to somewhere at the beginning of the makernote field for the makernote IFD to address the issue.

The following table summarizes the structures of the makernote field used by some vendors. Please let me know if you have additional information.

Make	Format	Header	Endian 1)	Offsets 2)	Ref	Remarks
Canon	IFD	None			[2]	Some CR2 images have a non-zero next-IFD pointer
CASIO	IFD	None			[4]
CASIO	IFD, at offset 6	"QVC\0\0\0"	Big-endian (MM)	Relative to the beginning of the makernote	[4]
FUJI	IFD, usually at offset 12	Starts with the string "FUJI" and a 4 byte pointer to the IFD	Little-endian (II)	Relative to the beginning of the makernote	[1]	Exif data uses big-endian (MM) byte order
Minolta, KONICA MINOLTA	IFD	None			[5]	Camera settings tag is encoded in big-endian (MM) style, regardless of the encoding style of the Exif data
NIKON	IFD	None			[3]	Models using this makernote include E990, D1
NIKON	IFD, at offset 8	"Nikon\0" followed by two bytes of unknown meaning			[1]	Models using this makernote include E700, E800, E900, E900S, E910, E950
NIKON	IFD, usually at offset 18	"Nikon\0" followed by 4 bytes which look like a version code and a TIFF header	From makernote TIFF header	Relative to the start of the makernote TIFF header		Models using this makernote include E5400, SQ, D2H, D70, D100, D200. Makernote IFD of the D200 has no next-IFD pointer. (Is this a bug?)
OLYMPUS	IFD, at offset 8	"OLYMP\0" followed by two bytes of unknown meaning			[1]
OLYMPUS	IFD, at offset 12	"OLYMPUS\0II" followed by two bytes of unknown meaning		Relative to the beginning of the makernote
Panasonic	IFD without a next-IFD pointer at offset 12	"Panasonic\0\0\0"			[8]
PENTAX	IFD at offset 6	"AOC\0" followed by two bytes of unknown meaning			[11]
SAMSUNG	IFD	None		Relative to the beginning of the makernote
Sanyo	IFD	-	-	-	[6]	Not supported by Exiv2 yet
SIGMA, FOVEON	IFD, at offset 10	"SIGMA\0\0\0" or "FOVEON\0\0" followed by two bytes of unknown meaning			[7]
SONY	IFD without a next-IFD pointer at offset 12	"SONY DSC \0\0\0"				Seen in Jpeg images, e.g., from DSC-W7, DSC-R1
SONY	IFD	None				Seen in SR2 images, e.g., from DSC-R1

¹⁾ If not specified, the byte order of the Exif data is applicable.
²⁾ If not specified, offsets are relative to the start of the TIFF header.

Exif.org has another table with similar info and sample pictures: Digital Camera Sample Images. According to this source, (at least some) Ricoh and Kodak cameras do not write the makernote in IFD format.

References

[1] Exif file format by TsuruZoh Tachibanaya
[2] EXIF Makernote of Canon by David Burren
[3] Makernote EXIF Tag of the Nikon 990 by Max Lyons
[4] "Makernote" Exif tag of Casio by Eckhard Henkel
[5] Minolta MakerNote by Dalibor Jelinek
[6] Sanyo MakerNote by John Hawkins
[7] SIGMA and FOVEON EXIF MakerNote Documentation by Foveon
[8] Panasonic MakerNote Information by Tom Hughes
[9] Various Makernote specifications from the PHP JPEG Metadata Toolkit by Evan Hunter
[10] ExifTool, the most complete and up-to-date tool for reading and writing meta information in image files, by Phil Harvey

[11] EXIF: Pentax type3 Makernotes by Ger Vermeulen

[12] Casio MakerNote Information