Was hat Tom getötet?

English Translation

What killed Tom?

There’s a serious ambiguity here. In English the sentence means both “What killed Tom?” and “What did Tom kill?” Is there anything that can be done to the German sentence, other than providing a clear context, that will resolve this problem?

You’re right, and there’s not much that can be done about it.
One possibility is to replace “Was” with either “Wer oder was” or “Wen oder was”. By including “wer/wen”, the case becomes clear (nominative vs. accusative), but it also changes the meaning to include persons instead of just things.

Edit:
Another possibility is to use the passive:
Von was (or “Wovon”) wurde Tom getötet? - What was Tom killed by?
Was wurde von Tom getötet? - What was killed by Tom?

I’d either rephrase the sentence or use the passive voice.

Rephrased:

  • How did Tom die?
  • Wie starb Tom? / Wie ist Tom gestorben?

Passive (with several alternatives):

  • By what was Tom killed?
  • Wodurch wurde Tom getötet?
  • Durch was wurde Tom getötet?
  • Wovon wurde Tom getötet?