What is the treatment for clostridium (c diff) infection that is best and has fewest side effects?

Varies: Oral vancomycin and oral Metronidazole (flagyl) have both been used extensively. Each has its pluses and minuses. The best answer would be which one works for the patient involved.

C.difficile tx's: By "best" do you mean optimal efficacy, but cost is no factor? By "fewest side effects" do you mean best tolerated but efficacy is less important? Are you looking for antibiotics, probiotics, donor stool enemas (yes, these actually work for c.Diff), only fda-approved regimens, short-course treatment, or novel techniques? Appropriate questions to ask your doc, w/whom you can share your concerns.