An allophone is one possible variation of a spoken sound used to pronounce a phoneme in a language. Some allophones cannot be substituted for each other (complementary), while others may be chosen at the preference of the speaker (free-variant).

For example, in English, aspirated and non-aspirated stop consonants are complementary allophones of the same phoneme ([p] in spin and [pʰ] in pin both correspond to /p/).

Free-variant allophones are important characteristics of an accent or dialect, famously seen in tomato (AmE /təmeɪtoʊ/ vs BrE /təmɑtoʊ/)

The dotted circle, ◌, is a typographic character generally used as a placeholder, or to show how a diacritic would combine with another character.

For example:

ؙ◌

The ḍammah is used in the Arabic script to indicate a short /u/ vowel (or its allophones)

◌̧

The cedilla is used mainly in Romance and Turkic languages to indicate the pronunciation of a letter is modified (or to create a new letter altogether).

◌̚

An upper-right corner diacritic is used in phonetic transcription to indicate a stop consonant with no audible release.

Reference

Wikipeda - Allophone Chart with pronuncations for characters in the International Phonetic Alphabet