Position of infixes of names (e.g. “van”) in bibliographies

Unfortunately, it's complicated. The proper organization and alphabetization of names is dependent on the identified nationality of the person in question. Thus, a German "van" name is handled differently than a Dutch "van" name. It may change further again upon immigration, e.g., Americans of Dutch or German origin typically follow English conventions or even remove the space.

Here is a nice guide to navigating these muddy waters, as well as a question from the German Language SE.

This answer may be a little disappointing, but I’ll give it a try:

I assume that the author’s name is [First Name] [infix] [Surname] (omitting other possible pecularities for simplicity’s sake) and you want to decide between the following ways of citing:

[infix] [Surname], [First Name]
[Surname], [First Name] [infix]

Obviously, your question boils down to whether the infix is considered to belong to the surname or the first name, i.e., whether the first name is [First Name] [infix] or the last name is [infix] [Surname]. Now, in all European cultures/languages that I am aware of, such infixes go with the surname. Moreover, I am not aware of anything comparable in other cultures.

Now, I cannot possibly know every styleguide, but given the influence of European cultures on academia, I do not expect many to group the infix with the surname as a default or general rule. Going by this answer, at least some seem to do this, however. Moreover, the bibliography software BibTeX considers every non-capitalised part in a name a prefix to the surname by default.

However, if there is a culture in which such an infix does not belong to the surname, I would consider it appropriately to group it differently. As already mentioned I am not aware of any culture that does this (but you could probably ask for this on Linguistics).

What is much more problematic than listing is sorting, i.e.: do you ignore the infix when sorting or not? Even for a given language, there may be different approaches to this. You could devise some complicated rules here that treat names differently depending on their origin, but I consider this a horrible idea: As you cannot expect readers to be familiar with those rules, not using a consistent approach for all languages here is a disservice to them, as they are more likely to search entries at two positions. After all, facilitating the look-up of entries is why we bother with sorting in the first place.

Finally, note that infixes may also occur in between two parts of the last name, e.g., in the German surname Schmoll genannt Eisenwerth.