In permineralization (fossil preservation, altered remains), is there a good substitute for silica (quartz)?

Answer 1

Do you mean:
A. Are there minerals other than quartz (or chalcedony, other form of silica) that also can replace remains? Yes, but commonly not as colorful. Pyrite, calcite or aragonite, for example. You may have seen some pyritized shells before--very pretty.
B. Can body parts made of silica be replaced by minerals other than quartz? Well, radiolarians or some sponges, for example, have shells or spicules made of biologic form of opal (hydrated silica)--which can be replaced by calcite(or other carbonate), pyrite, or phosphatic material, for example, rather than by quartz (or chalcedony).

Answer 2

Please check this link:
http://www.geol.umd.edu/~tholtz/G331/lectures/lecture2.html

I believe that first calcification, then silicification is the normal pathway (timewise).

As far as changing a silicified fossil to some other mineral system, I don't have a clue.