Our hope has diminished.
Nothing wrong here. We use the word diminished with emotions often, particularly when the diminishing emotion is positive. When things are getting better, though, we might not be as likely to say, "Our despair has diminished", instead saying something more like, "Our despair has lifted."
Please diminish your voice.
Definitely not. As individuals, we lower our voices, not diminish them. That said, I think it would be okay to talk about crowd noise diminishing. We walked away from Times Square, and the voices diminished. I wouldn't have any problem with that sentence.
Our sugar supplies have diminished.
You may notice I took the liberty of substituting storage with supplies. Storage doesn't diminish, but supplies can. That said, my revised sentence seems to have a very formal register. I would never say that in my own kitchen, but an executive in a chocolate factory might: "Our sugar supplies are diminished; if the trucks don't get here with a new shipment soon, we'll be forced to shut down the production line."
The flooding has diminished in our area.
This is a tricky one. It seems grammatical, but I don't like it – probably for idiomatic reasons. I think I would say instead, "The flooding has receded in our area", which is a more descriptive word, and one my ears are used to hearing being used with flooding.
Diminished means, "to make or become less," but your question brings up an interesting point: that it can sound very awkward when applied to the wrong thing, such as misery, or flooding, or the volume of our music.
2) Could you please put the pen on the book?
is the most likey way someone would say this. 3) "upon" is also OK but is more likely to occur in literature. These refer to placement.
1) Could you please put the pen over the book?
4) Could you please put the pen above the book?
These refer to location. This would imply the pen is located above the book, which would not be likely in the setting of your examples, but could be possible with other wording. For example:
Could you please put the pen on the shelf above the book?
Finally -
5) Could you please put the pen up the book?
does not make sense in this phrase. "up" refers to inside in a sense.
An example where it would be OK:
Could you please put the medicine up your nose?
Best Answer
Short of consulting other resources or data sets that show English word usage frequencies, the long-term answer is to read as much as you can. As with any language, English speaking children go through school reading books with many words they do not understand and often don't take the time to look up unfamiliar words in a dictionary. However, after so much exposure to words, if they were to see them as synonyms in a thesaurus for a word they did know, they would intuitively know which words they had encountered more often in their life and therefore which ones were more likely to be idiomatic or correct. You can replicate this experience, to a certain degree, by increasing your exposure to English that contains words you don't understand but can get a sense of with context clues.
As for your examples, in American English, the words "attractive" and "charming" would be the most common and relatively neutral in connotation. "Attractive" is by far the most common, and thus would be the most likely to use in a conversation. The word "fetching" is not common in American English usage, and the word "bewitching" bears an additional connotation that a person's beauty is so intense as to deprive its beholders of self control.