Grain filling has been the bane of woodworking (finishing) for about as long as we butchers have been at it.
I think it's important to keep in mind 2 things when choosing any finishing system, as they are frequently not "mix-n-match" compatible.
First; what look are you after? Do you want to fill the grain with an opaque/colored material, or do you want the true natural appearance of the wood to show. They are two different looks-neither good nor bad- just different.
Most of the paste fillers already mentioned are of the first category (opaque). Of all of these the most user friendly and non toxic one I've found is the water based material that comes from LMI. I've used the dark rosewood color and it is a pleasure to use. There is some grain lifting, but you're going to sand anyway so it doesn't matter. It is expensive, but it goes a long way. I put it on with a "plasticator" that I get from the auto body paint store.
For the clear fillers the choices are somewhat more limited . As said, epoxy has become the darling, but if you are having alergic reactions to it then it's out. When I've used exoxy I'll put Cabosil (
http://www.eagerplastics.com/cab.htm) in it to give it some body, which reduces the # of coats necessary. I suppose you could try putting Cabosil into a different (less allergic) medium such as shellac or even a waterbased finish like ktm, but I have never tried it. Could be worth a shot.
The old school filling method was to shoot finish- and alot of it. You would spray a couple coats of sealer, scuff it to take off the fuzz and then shoot 6 or so more. Sand and repeat.
A very important thing to keep in mind when finishing is compatibility of all the components. I use Sherwin Williams products because they have a professional division nearby that stocks their full line of products. With the exception of Trans Tint for shading the topcoats (which has proven to be very reliable) I use the S-W dyes, stains, sealer, and lacquer. I even use their thinner to reduce. This way I'm sure there will be complete unity of all the materials. I rarely ever have fisheye or other problems that were common when I used to use different brands of materials.
-C