According to the official description of the PED file format:
You can add a comment to a PED or MAP file by starting the line with a # character. The rest of that line will be ignored. Do not start any family IDs with this character therefore.
However, if you try to import into PhenoTips a PED file with comments (such as the attached example), you get "Error importing pedigree: Unsupported feature: multiple families detected within the same pedigree".
This is unfortunate because a comment line at the top of the file is an easy way to label columns when importing and exporting from a spreadsheet program.