This is an expression whose meaning, I feel, might best by explained by illustration. We cannot say that it means 'in good faith' and then insert it into a sentence. It is an adjective that, in my eyes and experience, goes a bit further than saying 'in good faith'.
If I were to read, 'a bona fide complaint', I would personally take that to mean, 'a bona fide complaint as opposed to a dodgy/shifty/fraudulent/etc. one'.
So if we are talking about a bona fide purchaser, we would be talking about an honest/genuine/legitimate purchaser as opposed to, for example, a fraudster.
e.g. 'If we can establish that they are bona fide purchasers, they will be able to keep the house.'
'Bona fide' was originally a legal phrase. In its legal sense, this example refers to a decision made honestly/genuinely/legitimately as opposed to, for instance, one made corruptly.
e.g. 'The Court concluded that the Minister's decision was bona fide.'
Note that the words 'honestly', 'genuinely' and 'legitimately' are used to illustrate the phrase's meaning rather than to define the phrase itself. In a legal context (and this is the context by reason of which I am quite familiar with the phrase), the definition of bona fide may vary among different jurisdictions and among different areas of law. Ultimately, the meaning of the phrase (in the legal context) will depend on the legal test used (in that particular jurisdiction or area of law) to decide whether or not something or someone is 'bona fide'.
I have seen 'bona fide' used also as an adverb e.g., 'Provided that the contract was made bona fide, we stand a good chance in court.' (Me --> as opposed to a contract that was not made bona fide). I have just learnt that the phrase was initially an adverb and that centuries of poor usage resulted in its modern use as an adjective.
Briefly, the phrase 'bona fides' is a plural noun, with a comparable definition to that of its singular adjectival form i.e. 'bona fides' means good faith as well as honesty, genuineness and legitimacy. A lawyer might say to his/her junior, for example, 'Have you checked the bona fides of that contract yet?' The junior might reply to the lawyer, 'Absolutely, the contract is bona fide' - and there we have our adjective 'bona fide'!
Finally, notice that I just said, 'bona fides means good faith...' Bona fides is a plural noun but I used a singular verb. I did this instinctively but I thought I should check the point to make sure that the use is correct. It seems that you can use a singular or plural verb with 'bona fides' - http://dictionary.reference.com/browse/bona+fides.