"Was wondering" + present tense (tense concordance?)

All of those sentences are correct if you are speaking in past tense about an action that continued for some time. Since "wondering" about something would take place over a period of time (probably minutes) then you can use it as you describe.

This article should help you: http://www.englishtenses.com/tenses/past_continuous

All three sentences are perfectly grammatical, although the verbs' tenses are a bit confusing.

I was wondering what she thinks of me.
To explain the tense disagreement, we need to look at the situation temporally. If you "were wondering" something, you wouldn't have to wonder about something also in the past—you could wonder about something that will happen in the future.

In our case, the future, in relation to the past-tense, is the present tense: thinks.

It's a little confusing, but it's basically just based on the situation described in the sentence.

Indeed, we don't need to wonder about something in the past but isn't this when the wondering takes place in the present? I mean I think if the sentence is "I have been wondering", it will be more grammatically acceptable, especially in formal contexts.

Yes, the sentences are grammatical. As to the meaning, it depends on the context.

I was wondering could refer back to an occasion in the past when you spent time thinking about something. For example, I was wondering this morning what she thinks of me, but now I've decided I don't care one way or the other.

However, the I was wondering phrase often has nothing to do with past contemplation. It is used to make a present request or ask a present question. So, when you say to someone (e.g. your boss) I was wondering if you agree with me, you mean simply Do you agree with me?

The past tense (indicating remoteness) removes the directness of the request or question. The progressive form further distances the question, cf. I wonder if you agree with me.

Still more distanced and deferential would be the past tense in both clauses: I was wondering if you agreed with me.

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Swan in Practical English Usage has a good section on this topic, entitled Politeness: distancing verb forms (p411).

1. past tenses: How much did you want to spend?

We can make requests (and also questions, suggestions and statements) less direct (and so more polite) by using verb forms that suggest 'distance' from the immediate present reality. Past tenses are often used to do this. I wondered if you were free this evening.

2. progressives: I'm hoping ...

Progressive forms can be used in the same way. They sound more casual and less definite than simple forms, because they suggest something more temporary and incomplete. I'm hoping you can lend me £10. (less definite than I hope...)

Past progressives give two levels of distancing: Good evening. I was wondering: have you got two single rooms?