While using Rikaichan, one invariably notices all the words just consisting of
one kanji character with its onyomi reading. However, most of these words seem
to be barely used (at least in real conversations). It seems to me that most
are only used in scientific papers as abbreviations for the respective jukugo
of the same sense.

One character kanji words that are actually usable in conversation (and that
don't make you sound super scientific) seem to be 敵, 詩、毒 and 罰, for example. I
think I've also heard 地, but there are other synonyms whose usage is
definitely preferred. Furthermore there are some kanji that only seem to be
used in fixed expressions like 気 in its various idioms and 念 in 念のために(so they
don't really count here).

So, how should I think about these words? Are they just newspaper
abbreviations (much like 独 for Germany, etc.) that shouldn't even be
considered as real words? Are there any general guidelines which words one
indeed can use in conversations (Or maybe even an explicit list of all such
words which are common 話言葉、since there seem not to be too many)?
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words usage kanji
Onyomi words consisting of just one kanji (and nothing else)
As I commented above, there are **so many** on-yomi words consisting of
nothing else but single kanji. Let us start with those that even small
children could use actively in their conversations.

・円{えん} = circle, yen

・駅{えき} = train station

・肉{にく} = meat

・服{ふく} = clothes

・本{ほん} = book

・変{へん} = strange

・列{れつ} = line (of people, objects, etc.)

・礼{れい} = bow, etiquette

・番{ばん} = turn (as in "It's my turn.")

・席{せき} = seat

・曲{きょく} = song, tune

・県{けん} = prefecture

・行{ぎょう} = line(s) in writing

・会{かい} = gathering, event

Trust me, there should be many more.

Moving on to the ones it might take adult speakers to use actively..

・愛{あい} = love

・死{し} = death

・法{ほう} = law

・具{ぐ} = ingredient

・悪{あく} = evil

・軍{ぐん} = army

・恩{おん} = favor, moral indebtedness

・案{あん} = idea

Gotta stop here; It's past midnight.

Seriously, if I had the time and energy, I could make this list 10 times as
long without much difficulty.
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The fact that the overwhelming majority of on'yomi words is compound does
_not_ imply single-on'yomi-kanji words are rare.

Let's think about it in English. English has imported a huge number of Latin
and Greek words, most of which is compound (though they aren't necessarily
disassemblable in the scope of English). Picking up from your question:
_invariably_ (in-vari-abl-y), _character_ (charac-ter), _conversation_ (con-
vers(-a)-tion) etc. Meanwhile, there are also many words that is likewise
single words in original languages, and some among such shorter words are so
basic and heavily used that hard to find replacement in present-day English,
such as _use_ , or _sense_ , or _sound_ , or _fix_ , or _just_ (all from your
text too).

The situation is same in Japanese. Replace Latin with Chinese (on'yomi) and
you'll get many basic words only take single kanji. The number is finite, but
not sure if it's pointful to make a full catalog of them (though I don't know
if you closely printed them on an A4 sheet with 6pt font...) Besides
@l'électeur's great collection, I can easily think of any random word as much
as you want:

> 客（きゃく） "guest; customer"  
>  便（べん・びん） "a transport of car/train/plane/ship; convenience; feces"  
>  図（ず） "figure; chart"  
>  表（ひょう） "table; list"  
>  文（ぶん） "sentence; passage"  
>  塔（とう） "tower"  
>  金（きん）・銀（ぎん）・銅（どう）・鉄（てつ） "gold, silver, copper, iron"  
>  as well as 一, 二, 三, ... 十, 百, 千, 万, 億 etc. etc.

**PS**  
気 and 念 you mentioned are not useless words alone. These words are merely
being cast out from modern material life. If you read some fantasy or science
fictions, you'll soon find 気 ("aura, energy, qi/chi") and 念 ("psychic,
spiritual power") used all by their own.
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