How can I reheat a roux-based (alfredo) sauce in the microwave without separation?
Sunflower lecithin (sorry, best link I could find) is gaining in popularity as an alternative to soy lecithin because it is widely perceived to have a neutral taste and actually has superior emulsifying properties.  It's a little on the expensive side, though.

Soy lecithin by itself doesn't taste horrible if you buy it as a food additive (as opposed to a nutritional supplement).  It's common to find in a lot of popular frozen pasta-and-sauce dishes, such as Michelina's, which obviously must be microwaveable without the sauce curdling or separating.

Another option is Sodium Stearoyl Lactylate, if you can get hold of it.  This one adds a little sweetness which is generally pleasant-tasting, or at least inoffensive.  You'll find it used most often as a dough conditioner or in baked goods, but another popular use for it is in commercial sauces, although unfortunately I can't find specific examples right now.

But probably the best emulsifier for what you're trying to do here is xanthan gum.  It's also used as a gelling agent, but in small quantities works as just an emulsifier.  You can find it, for example, in this Bertolli Creamy Alfredo Pasta Sauce - exactly the sort of thing you're making.  It's also used in the Stouffer's Alfredo sauce.

Mix in a little lecithin or xanthan gum as an emulsifier while the sauce is fresh or cooking and it's very unlikely that your sauce will separate, either in the fridge or in the microwave.

As for what you can do to specifically prevent separation while reheating, if you didn't add any emulsifiers in the first place... I really don't think there's anything you can do.  If you're a slow enough eater the sauce will eventually separate right in front of you; that's just what happens when you have water and fat in the same sauce.  Best to reheat on the stove top in that case, and stir frequently to prevent any further separation.