If a cupcake is filled with a chocolate mousse or ganache, does it need to be refrigerated? If they do, how long can they stay out for? What other non-refigerated fillings would you recommend? TIA!!
Mousse - yes, it probably needs to be refrigerated. Depends on your recipe.
Ganache - no, that can stay at room temperature for ~3 days.
As to other fillings, it depends on what you're going for. Preserves, American buttercreams...there are tons of options. 
Not all things that contain milk need to be refrigerated, otherwise you'd be buying candy bars in the refrigerator section at the grocery store.Something about the sugar content stabilizes/preservers the milk, Doug has explained it very well here and there in the thread universe. Here's one: http://imgsrc.cakecentral.com/cake-decorating-ftopict-646205-.html
Wow, thanks for the link. That sure had a lot of info. Anyone has any suggestions on what to fill a yellow cake? I don't really want to use buttercream since that is going on top and I prefer something that doesn't need to be refrigerated.
If I'm ever at a loss for flavor ideas, I scan through the "big list"
http://docs.google.com/Doc?id=df4f9hbq_46cs9f28fs
You should be able to find all sorts of fillings there!
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