Earlier quoted context omitted.
Apart from all the silent letters, which are fairly regular (and I assume is what you're getting at) there's a fair number of pronunciation exceptions. See the different ways of pronouncing "tous" or the different words that have irregularly silent "l"s (e.g. fusil) and other irregularly silent consonants in the middle of words (e.g. automne). French has quite a lot of exceptions to its pronunciation rules in additio…
Those are some good examples, you're right. It is quite a bit less regular than I remembered from my high-school days. For 'er' though, isn't the rule essentially that it is pronounced 'a' at the end of verbs, and 'ar' otherwise? I realize that is not a phonetic rule, though.
I don't know of any regular, even semantic, rule off the top of my head that covers when it should be pronounced which way for non-verbs. I wonder if someone more versed in French etymology could find one.