I agree with JSWolf that ePub is the better format to archive (and therefore to buy). However, many publishers still target the least capable format (MOBI), and so there may be little difference between MOBI and ePub in any given ebook. So I would not hesitate to buy from Amazon if the Kindle version is significantly cheaper, and sometimes only Amazon has a particular ebook.
At one time I avoided TOPAZ, but now I buy this if it is the only option. Conversion from TOPAZ to ePub is not perfect, but often good enough.