Calibre

[speakingtohe]

space between paragraphs, indentation of paragraphs, ligatures, margins etc.

The way I like mine, and it is not a very popular way is:

Space between each paragraph
Left justified with no indent.

It may seem at a glance to make the book longer (more page turns), especially if there are a lot of one line paragraphs, but it adds around one extra page per 100 or less.
I have tried a dozen things but this is the most comfortable to me.

If you have the keep original file tweak set to TRUE it will never overwrite your original, which would have saved me a lot of grief if the tweak had been available earlier.
Makes it easier to try different things.

Preferences->tweaks last one on the list.

The formatting options are mostly under look and feel.
My default settings: Preferences-common options-look and feel

I check remove spaces between paragraphs.
I check insert spaces between paragraphs.
I check keep ligatures (only useful for some PDF but doesn't hurt)
I check translate Unicode characters. (Fixes some font problems in some files but mostly doesn't matter)
line height (for blank lines) .03 em
Indent 0.0 em

Will not work on every file, but about 95% and if you set them in preferences, then you don't have to change them every time.

And you will probably prefer your books different than I do, just giving you an example.

You can also fix individual books with tweak epub, and search and replace to get rid of those pesky headers which some books still come with, but not usually necessary these days.

Helen