The most common ways of representing Ancient Egyptian are hieroglyphs and their Latin transcription.
The total number of hieroglyphs, for example recorded in Hieroglyphica, is nearly 7000. They have not yet been put in Unicode, though a proposal to cover a basic set of about 1200 of them is in the works. In the meantime, the solution is to use custom non-Unicode fonts along with special editing programs that let you arrange the symbols in the various ways they are found naturally. On OS X, MacScribe can be used for this. An example of how it works can be seen here.
For Latin transcription alone, Unicode is possible. The most common standard alphabet currently used has 24 letters (all consonents, no vowels):
ȝ ỉ y ʿ w b p f m n r h ḥ ḫ ẖ s š ḳ k g t ṯ d ḏ
10 of these are not found in English. They can all be entered via the Character Palette in OS X, but it is a lot easier to use a custom keyboard, such as the EgyptTrans.keylayout you can download from my iDisk. There are also transcription systems which use only ASCII, such as found in the Manuel de Codage. MacScribe uses a system like this for input.
Egyptian was also written in the hieratic and demotic scripts and in Coptic. For the first two I am unaware of any Unicode proposals or fonts, but Coptic is in Unicode 4.1 and you can download a Coptic2005.keylayout from my iDisk. You also need one of the fonts that covers Coptic -- ALPHABETUM Unicode, Code2000, MPH 2B Damase, or New Athena Unicode.