Number formatting: use of digit separators in manuscripts

Digit separators differ between countries, particularly since the decimal seprator is comma in many countries but a period in English/American. Hence in English you may use commas as digit separators while in other countries periods are used. Space is therefore the only separator that is not confusing. A general rule of thumb is to not use separators for single-thousands but start to use them for tens of thousands and up

1000

10 000

100 000

1 000 000

When using spaces in writing, it is good to remember to use non-breaking spaces so that numbers are not broken over lines.

In scientific literature it is common to employ a small space to separate groups of digits (see e.g. NIST SP811). If you're using LaTeX to write your articles you can obtain this spacing in two ways:

1. Directly with the small-space command \,. For example: There were $10\,000$ people at the concert last night (well, not exactly a scientific example).
2. Using the siunitx package and the command \num (or \SI for quantities with units), which can take care of the spacing automatically. For example: There were \num{10000} people at the concert last night (it adds automatically a small space after the 10).

I think that, in as much as there is such a standard, it tends to breakdown between scientific and humanities fields. In general, I would argue that the modern standard in science is to use only spaces as separators ("2 500" instead of "2,500" for instance), while the reverse tends to be true in the humanities.

However, the best guidelines for these sorts of issues, as usual, is to consult with the guidelines and recommendations of the individual publisher.