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

computation and writing

keyboard lay out (lots of ads)
Chen's typing aid that can be used to send Arabic email from any keyboard

On line dictionaries
sakhr has vowels