Flagyl does treat some gut parasites. I was put on it for a gut amoebic infection when I was a teenager.
Red clover is a blood cleanser that apparently also helps get rid of parasites.
Vitamin C (esp. if given by IV) in high doses may drive out parasites.
Anti-parasitic herbs: garlic, wormwood (artemesia), black walnut hulls, pumpkin seeds, grapefruit seed extract, hyssop, goldenseal, quassia bark (inhibits protozoa), elecampane, echinacea, fennel, barberry, oregan grape, goldthread (coptis chinensis), butternut, calendula, cat's claw, chaparral, cranberry concentrate (kills protozoa), ficin (ficus glabrata), ginger (kills blood flukes, too), horsemint (monarda punctata), olive leaf, pinkroot, pomegranate, propolis, sage, sarsaparilla, senna, tansy, turmeric, yellow gentian.
Most of these herbs are mentioned on http://www.innvista.com/health/microbes/parasite/treatpar.htm
Essential oils: tea tree, patchouli, peppermint, lavender, clove, oregano, anise, fennel, nutmeg, thyme.
Probiotics are important.
I've heard that protease enzymes taken on an empty stomach can be very good for cleansing the body.
UV blood treatments are also used to treat blood parasites at some clinics. And I would think that IV ozone and/or hydrogen peroxide would also kill parasites in the blood. Colloidal silver is another anti-parasitic.
Eliminating sugar from the diet can be helpful, too.
Chronic Lyme Disease, Gluten & Sulfite Sensitivity, Many Food/Inhalant/Medication/Chemical Allergies & Intolerances, Asthma, Gut issues (dysmotility, non-specific inflammation), UCTD ("Secondary Lupus-Like Syndrome"), Osteoporosis, Pancytopenia, chronic malabsorption/malnutrition, etc.; G-Tube; Currently TPN-dependent.
Meds: Zofran, Pulmicort, Heparin (to flush PICC line), Claritin, Colloidal Silver (used topically), IV Milk Thistle, probiotics.