Learn Russian: Это историк, которого я очень уважаю. - This is the historian whom I respect very much.

Которого is in the Accusative case because it is the direct object of the verb уважаю (I respect). Even though the historian is the main focus of the first part of the sentence, in the second part he is the person being respected. The pronoun representing him must take the Accusative case to show that he is receiving the action.

Wait, doesn't которого look exactly like the Genitive case ending?

Yes, it looks identical! Because историк (historian) is a masculine animate noun (a living being), its Accusative case takes the exact same form as its Genitive case. The relative pronoun must match the animacy of the noun it replaces, so it also uses this Genitive-looking ending for the Accusative.

How do I know whether the pronoun should match историк or я?

A relative pronoun always gets its gender and number from the noun it refers back to in the first half of the sentence (here, the masculine singular историк). However, it gets its case from what it is doing in its own part of the sentence (here, being respected by я, which requires the Accusative case).

In English, we can just say "the historian I respect" and drop the word "whom." Can I drop которого in Russian?

No, Russian never drops the relative pronoun. You must always include the correct form of который. You also must always put a comma before it to separate the two parts of the sentence.