I would have thought so. I wanted to do just this a few months ago because we release an MP3 and an OGG Vorbis file for each show. Turns out that the RSS spec only allows for a single enclosure element per post.
Yeah, that's geek talk, but suffice it to say that your actual media file is wrapped in enclosure tags within your post. Podcatchers know what to do with this enclosure tag and they download the file that it points it. Podcatchers also only expect one media file per post so if you put two in, you're asking for trouble.
In practice, I suspect that most podcatchers would just ignore the other enclosure element, but some of the less robust ones may actually crash.
What I ended up doing on the JaK Attack! site is creating two feeds: an MP3 feed and an OGG feed. I used the categories feature of my blogware to create an MP3 and an OGG category and then I pushed the feed for each category into Feedburner. Now my listeners can subscribe to whichever one they want.