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There are several uses of the small っ:

  • Compounds with the first kanji ending in つ or ending in consonant + 'u' with the second kanji beginning with the same consonant: the elision of the 'u' happens naturally and ended up being written
  • Euphonic modifications (e.g. -て form)
  • Foreign words in katakana aiming at matching foreign pronunciation

Are there others? Is it always phonetic (e.g. elision) or are there other possible reasons? When in history did this happen? Can it also happen inside kun'yomi words (ignoring grammatical aspects)?

  • I am not writing an answer because I don't have much evidence for this idea, but it makes sense when you consider the combination of on readings. e.g., 発見 is read hakken but the individual characters are hatsu and ken, and this happens pretty predictably with Sino-Japanese words. – Casey May 22 at 18:02
  • The big つ had a baby! :) This also happens with other characters as well. – JACK Oct 9 at 22:27
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The history has been covered previously as mentioned in a comment by broccoli forest, so I'll answer your question about its usage.

So:

  • Yes, it can be used in kun-yomi, even if combinations like 掻っ攫う are ignored.「全く」,「全{まっと}うする」 and 「驀地{まっしぐら}」 are the only ones I could come up with off the top of my head, but I'm sure I've seen other similar words as well.
  • Another usage is to express a "sharp" tone. E.g.「くそッ」would indicate a 'sharper' or more 'intense' tone than「くそ」(which could in some cases be spoken with a relaxed/flat tone as well). Link to relevant question.
  • The sokuon is also commonly used to indicate glottal stop (or really, a sound that kind of resembles a glottal stop), e.g. as a reaction that indicates shock or exasperation or some other strong emotional response that is not converted into words for one reason or another. In actual use it can look like 「っ……」or「っ……!」etc.

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