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Whenever I see 「よく」, I have to ask someone whether it means "often" or "good".
For example, here is a sentence from my book:
クラスへ行って、先生の講義をよく聞いて、ノートをよく取り、それをよく覚えれば、試験でいい点がもらえる。
I thought all three 「よく」s meant "often" (eg. "often takes notes"), but a Japanese friend said they all mean "good" (eg. "takes good notes"). He said "often takes notes" would be 「よくノートを取り」. However, he doesn't know why.
How can you tell the two usages apart?
As Yuu wrote, there is a tendency that よく immediately before a verb often means “well” and that よく at the beginning of a sentence often means “often,” but it is by no means a firm rule. Word order is one of the clues, but in the end, the distinction depends on the context.
For example, suppose that someone said
よく先生の講義を聞いていれば、試験でいい点がもらえる。
Does it really mean “You will get a good mark on an exam if you are listening to your teacher’s lecture often (like two thirds of the time)”? It may, depending on the context, but I think that in most contexts, it is more likely that the speaker meant “You will get a good mark on an exam if you are listening to your teacher’s lecture carefully,” even though this means that the speaker used a slightly less natural word order.
It's the placement of the frequency word (よく).
先生の講義をよく聞いて -> Listen well
よく先生の講義を聞いて -> Often listen
ノートをよく取り -> Take good notes
よくノートを取り -> Often take notes
それをよく覚えれば -> (If) Remember well
If you don't see the pattern yet, よく + verb (directly preceding the verb) would generally have the connotation of 'well', while よく anywhere else in the sentence would likely be 'often', with the focus of the sentence shifted elsewhere.
良く, yoku, means both "frequently" and "well". It's the same kanji as yoi but in the adverb form. If you think about doing something well as being similar to doing it thoroughly and doing it thoroughly as similar to doing it often perhaps you can see the relatedness of the two concepts. One of the pleasures of learning a new language is that it makes you think outside your accustomed modes.
