As merely a standard (ignoring implementations), of the amendments to ISO 639:

1. Alpha-1:1998 is deprecated and rarely utilized;
2. Alpha-2:2002 is the basis of BCP 47 (so is frequently utilized); and:
3. Alpha-3:2007 includes a significant amount more subtags and variants, frequently normalised to their corresponding ISO 3166 Alpha-3 counterparts.

Consequently, if possible, utilize Alpha 3, with a fallback to Alpha 2 where relevant standards necessitate it (an example is the aforementioned – BCP 47).