We have the following two tags:
There is a scientific difference in meaning between these two words (an allergy is a medical condition while an allergen is a substance that triggers it), but I'm not finding this difference useful on this site for actually classifying questions. A brief review of the questions on both of these tags appears to show no rhyme or reason for one to be used or the other - rather, it seems to be random and up to the whims of the posters rather than any specific criteria. Quite a few questions have both tags, and I cannot find anything that distinguishes them from questions that have just one of the tags.
I propose that we keep the more popular tag allergy and make allergen a synonym.