Problem: I would like to know when I should use a custom taxonomy vs when I should use a custom field. What are the advantages and disadvantages of each?
Solution:
One advantage of a taxonomy - archives can be generated automatically. There are no archives generated automatically for custom fields, though you could create them manually with Views and custom Pages.
Aadding a taxonomy item is fast - faster than the alternative.
With a (non-hierarchical) taxonomy I can add several, comma-seperated brands/companies (while I have to check myself if the terms are the same...).
Post relationship queries are marginally slower than taxonomy term queries.
It is possible to add many taxonomy filters to a custom search View. It is not possible to add more than one post relationship filter to a custom search View.
It is not possible to capture all information effectively with taxonomy terms. For example, dates are not easily converted into terms, and you can create more complex queries with dates.
Toolset's post relationships are proprietary. Taxonomy terms are common to all WordPress sites by default, so 3rd-party tools are more likely to integrate with taxonomy terms than with post relationships.