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.
Don't put the shrimp etc in the sauce in the first place and cook it separately, that way you don't have to take it out. Then just top your pasta with it and if say you are cooking meatballs and want a little sauce on them mix a little sauce in with your meatballs and then put them on top. If you want that mixed in with the pasta look then do the same thing I said above and mix the pasta in your individual serving bowls or plates if you are using one after you have dressed your pasta.
Your just not going to get an even distribution with random variables, all you can do is pick and count if you want everything evens.
Best Answer
If I plan on storing my pasta in the fridge with the sauce, I take the pasta out of the boiling water and immediately rinse it in cold water. I rinse until the pasta has cooled completely. Make sure to drain it well. Afterwards, I either mix a little sauce in the pasta to help keep it from sticking or just put the sauce on top. Basically I'm trying to stop the pasta from continuing to "Cook" in the sauce.