I could go either way, but lately I tend to use the conventional oven for re-heating. About the only thing I use my microwave for is heating up a bowl of canned soup, or heating any kind of frozen "tv dinner" type packaged meal. And of the latter, I try not to eat those terribly often. Campbell's Chunk Soup on the other hand, I eat moderately often.
Anyway, as to whether or not there's a noticeable taste difference... I don't know. Never really thought about it. For re-heating (as opposed to initial cooking) I wouldn't expect there to be much difference, but who knows?