Is there a single word for when something becomes neglected or forgotten (e.g. a plant dies because the gardener forgets to water it)?

I actually really like the word you used: I would refer to such a software program as defunct, especially if it might be resuscitated in the future. From Wiktionary:

defunct (comparative more defunct, superlative most defunct)

1. (now rare) Deceased, dead.
2. No longer in use, inactive.
3. (computing) Specifically, of a program: that has terminated but is still shown in the list of processes because the parent process that created it is still running and has not yet reaped it. See also zombie, zombie process.
4. (business) No longer in business or service.

Abandoned:

• carelessly disregarded without consideration for the consequences.

An unsupported program/software will end up useless because of lack of proper assistance:

• (Computing) (Of a program, language, or device) not having assistance for the user available from a manufacturer or systems manager.

(ODO)