Manual Transliteration Systems I have used

Arabic:: Library of Congress , International Phonetic Alphabet (IPA) (scroll to yellow), Foreign Service Institute (page 13 of Smith's 1969 Modern Written Arabic)
YIVO for Yiddish and Hebrew

Persian: SDSU Language Acquisition Resource Center LARC transliteration system and Dr. Atefeh Oliai's variations on this

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Russian: IPA

American Sign Language (ASL): SignWriting as used by researchers at the Salk Institute (La Jolla, CA)

Handling special characters

Embedding IPA and non-Latin characters so they display on a screen using Unicode