Abstract: A software application and user interface that is capable of inserting comments into a document with embedded objects and providing more complex comment options. An embodiment of the present invention is an application program on a handheld computing device or other computer. The user can insert complex comments into a document including muti-media and nested comments. The user can also do mathematic calculations within the comment without altering the existing content of the commented document. Another feature is a “scaffold comment,” which is a comment that has a pre-defined portion. The comments can have unique comment icons to readily show the user what type of comment is embedded in the document. Another feature is the nested comments can be stored as an XHTML file and viewed with an XHTML file browser.