• The Power of Prayer (Dua'), Hope, and Reliance on Allah
• The Use of Prescription Medicine
• Alternative Therapies
• Employing Islamic Hygiene
• Boosting the Immune System

The Power of Prayer (Dua'), Hope, and Reliance on Allah
Ibn Abbas narrated that a man came and asked Allah's Messenger (peace be upon him) what he should ask Allah upon concluding the obligatory salat. He answered, "Pray for good health." The man asked "Then what?" And the Prophet replied, "Pray for good health." The man asked again "Then what?" And the Prophet replied, "Pray for good health and well-being in this world and in the hereafter."

It is also narrated in Bukhari and Muslim that when Allah's Messenger (peace be upon him) visited a sick person in his family, he used to pass his hand over the person's head praying, "O Lord and Sustainer of human beings, relieve these sufferings and cure this servant. Indeed, You alone have the power of healing, and You alone can effect permanent recovery."
 

Recommended Reading:  Medicine of the Prophet by Imam Ibn Al-Qayyim Al-Jawziyyah Sickness: Regulations and Exhortations by Muhammad Al-Jibaly Islamic Medicine Online

The Use of Prescription Medicine
The use of Acyclovir is the most popular and widely used method of controlling herpes outbreaks through medicine. However, as with most medications, it does have side-effects. It does not cure herpes, but rather helps to suppress the virus so that outbreaks do not occur. It is commonly prescribed at about 400 mg twice a day. It is also rather expensive.

Some companies are trying to develop other medicines as well as vaccines which would help to prevent the spread of herpes to those who are not already infected.

Alternative Therapies
Allah's Messenger (peace be upon him) said: For every illness Allah created, He also created a cure. [Reported by Bukhari]

Several alternative/natural therapies have been recommended to help treat herpes: 
Hydrogen Peroxide - spraying hydrogen peroxide on the site oof the outbreaks twice daily. For more info on how this works we recommend the book Never An Outbreak, by William Fharel.

Taking the nutritional supplement L-Lysine (approx. 500 mg daily), or eating foods high in Lysine and avoiding foods with arginine which counteract Lysine. A specially formulated antiviral Lysine capsule has also been formulated.

Some have recommended placing a few drops of Oil of Oregano under the tongue. More on this can be found in the book, Life Saving Cures by Dr. Cass Ingram.

Other suggestions have included Red Marine Algae, Eating Mangos, and minimizing sugar which can actually be replaced with honey about which Allah said {{And from it's [the bee's] belly comes forth a drink of varying colors, wherin is a cure for people... [Qur'an 16:69]}} And the Messenger of Allah (peace be upon him) also said: "Make use of two remedies, honey and the Qur'an." And in another hadeeth recorded by Ibn Majah: "Whoever eats honey (at least) three times a month will meet with no great affliction."

Employing Islamic Hygiene

1. Eliminating sexually risky behaviors that will increase chances of transmission such as entertaining extra-marital affairs and taking appropriate precautions when choosing a spouse.
2. Making ghusl (shower for full body purification) immediately following intercourse and before sleeping, (this is a recommended Sunnah). 
3. Abstaining from intercourse during an outbreak (which in addition to being commonly recommended by physicians, can also be proven Islamically by analogy to the prohibition of intercourse during menstruation).
4. Removal of pubic hairs in accordance with the fitrah, (required at least once every forty days).

Boosting the Immune System
The immune system should also be stimulated in order to more effectively counter viral outbreaks. This can be done by taking vitamin supplements, eating garlic regularly, as well as black seed, about which Allah's Messenger (peace be upon him) said, "Use black seed regularly, because it has a cure for every disease except death." [Bukhari]