Question

where's the best place to indicate that an individual was adopted?

Answer 1

In the biography section.  This is, in general, the best place to explain anything that doesn't fit nicely into the pre-defined fields of the profile.

Here's the help page on adoption and other multiple parent situations:  http://www.wikitree.com/wiki/Multiple_Parents

Answer 2

I would put both known names on the persons profile.  Last name at birth (ex. Jones) and the preferred last name, or last name at death (ex. Smith- his adopted name.)  I would then explain the two names under his bibliography.