Which Buddha do Buddhists take refuge in?

None whatsoever. As Thanissaro says, any real insight is always a surprise.

It means literally accepting the Buddha as your refuge. Like how a child feels about his loving parents. When he gets into trouble, he will go to his parents. When he needs advice, he will look for his parents. He never doubts his parents or try to do DNA tests to verify if they are his true parents. :) Just like that, one should put his full faith in the Buddha in person and in his enlightenment to accept him as the only teacher who can show you the way to everlasting peace.

According to my teacher, which I feel is very much correct, we are taking refuge in the ideals of Buddha, Dhamma and Sangha. So whoever fulfills these ideals, we take refuge in them. Remember, that there were many Buddhas before Siddhartha Gautama.

So what are these ideals? It is easy to come across these ideals in the Buddha Vandana. It says that the Buddha is - 1. the one who is Arahant which is portmanteau of Ari (evils) and Hant (destroy) which means destructions of all evils.
2. the one who is Samma Sam Buddha - one who has become fully enlightened. 3. the one who is Vijja Charan Sampanno which means who is perfect in wisdom and moral conduct. 4. the one who is Sugato - the one who has travelled a great path 5. the one who is Lokvidu which is again a combination of Lok(in ancient India, it was not only the world which was called Lok but this body of ours was also known as Lok) and Vidu(intelligent, knower); thus a knower of the world and the body 6. the one who is Anuttaro who is incomparable 7. the one who is Puris Dhamma Sarthi - Puris means men/women and Sarthi means the one who drives - thus he is the one who has turned the wheel of Dhamma 8. the one who is Satta Dev Manussana - the teacher of Gods and Humans 9. the one who is Bhagavati - the one who is enlightened and blessed

Every Buddha who was ever born had these qualities and when we take refuge in Buddha, we take refuge in all of these qualities reminding ourselves of these virtues to be cultivated in ourselves.

Now we are spending the era of Gauthama Buddha. So we should take refuge on him. Vairocana and Amithabha are Bodhisattas(to be Buddhas). They haven't attain Buddhahood yet. So the Buddha we should take refuge on is The Sakyamuni Gautama Buddha.

When you take refuge you take refuge in the qualities of the Buddha. In more detail.

You have to take inspiration in the Buddha to to develop the qualities of the Buddha and the Triple Gem.

This interpretation may change from tradition to tradition.

I think both interpretations should be somewhat intertwined and doesn't need to be clearly distinguished. See, you'll not say 'I only take refuge in Gautama Buddha, but not Buddhahood', or 'I will take refuge only in Buddhahood, but not Gautama Buddha', both of these sounds weird. Buddha Gautama represents Buddhahood, so we can not separate Him from Buddhahood.

Abhidharmakosa-bhasya of Vasubandhu explains taking refuge in Buddha like this:

They who take refuge in the Buddha, take refuge in the factors (dharma) of the perfected being (arhat) that constitute a Buddha (buddhakāraka), the factors that are the causes of the designation “Buddha” [buddhaprajñaptihetūn], i.e., the factors due to which, as a principal cause, a certain person is called Buddha; or else the factors through the acquisition of which a certain person, understanding all entities, is called Buddha. These factors are (1) the cognition of exhaustion (kṣayajñāna), (2) the cognition of non-arising (anutpādajñāna), and (4) right view (samyagdṛṣṭi) (vi. 50, 67), (4) with the factors that accompany (parivāra) these cognitions (jñāna), i.e., with the five pure aggregates (skandha).

As for the material body (rūpakāya) of the Buddha, it is not subject to modification through the acquisition of the status of Buddha. Thus, one does not take refuge in the material body of the Buddha, which is, in fact, the material body of the Bodhisattva.

[Question:] – Does one take refuge in all the Buddhas or in one Buddha? [Answer:] – According to the nature of entities [lakṣaṇatas], and in the absence of an explicit declaration (kaṇṭhokti), [one takes refuge] in all the Buddhas, for the Buddhas have always followed the same path, (1) a mundane (laukika) path and (2) a supramundane (lokottara) path (vii. 34). [Lodrö Sangpo translation.]