The click languages with the largest numbers of speakers are Zulu (with 10 million L1 speakers) and Xhosa (8 million). They both use three basic types of click (dental, alveolar/retroflex, and lateral), and have a long-standing orthographic tradition of spelling them as c, q, and x respectively.
The simple letters c, q, x represent the voiceless clicks, i.e. the clicks pronounced with accompanying [k]. They can also be aspirated (i.e. with [kh]), voiced (i.e. accompanied by depressor [g]), nasalized (accompanied by [ŋ]), or breathy-nasalized (accompanied by depressor breathy-voiced [ŋ(g)]). These are written respectively ch, qh, xh; gc, gq, gx; nc, nq, nx; ngc, ngq, ngx. (You can listen to all the series except the last pronounced by a native speaker here.)
Until 1989 these were written in IPA with the special symbols [ʇ], [ʗ], [ʖ]. I think these symbols may have been devised by Doke, whose Phonetics of the Zulu language came out in 1926.
Meanwhile missionaries and linguists dealing with the Khoi-San languages adopted a different notation system, writing [|], [!], [ǁ] for the clicks used in the Nguni languages (Zulu, Xhosa etc.) plus [ʘ] and [ǂ] for bilabial and ‘palatal’ clicks found only in the Khoi-San languages. These symbols were designed so as to be typable on the typewriters of the day: instead of | and ǁ people mostly wrote / and //, using the backspace key to create ! out of an apostrophe and a full stop, and ǂ out of the equals sign and /.
So as of early 1989 we had three notation systems. But at its Kiel Convention in 1989 the IPA, at the instigation of Peter Ladefoged, decided to go over to the Khoisanist symbols, which are what you will now find in IPA publications.
Wikipedia somewhat contemptuously remarks
At one time, the IPA was augmented with a set of Latin-based symbols for clicks, but they were never much used, and were eventually given up for the Khoisanist symbols.However, it is not true that “they were never much used”. Generations of phonetics students from the twenties to the eighties learnt and used them (as I did myself). Everyone qualifying as a speech therapist in Britain had to know them. I myself must have taught them personally to close on a thousand students. Conservatively, I would estimate that at least 25,000 people were taught them, many more than ever worked with Khoisan languages.
I think the IPA was misguided in making this change. The old symbols were better.
Just look at these screenshots (from Wikipedia).
As you can see, the symbol for the dental click, the pipe |, can look dangerously like a sanserif lower-case l. The symbol for the lateral, the double pipe ǁ, can look like double lower-case ll. And both are also widely used for a quite different purpose, namely as intonation phrase boundary symbols.
No such danger with ʇ and ʖ.
Bring back the old IPA click symbols!
(Oh, and that’s an exclamation mark at the end, not a retroflex click.)