I believe condoms are less effective (although still highly-effective) in preventing Herpes, HPV and Molluscum Contagiosum compared to bacterial STIs, and HIV. HIV actually transmits poorly during sex compared to other viruses; intact skin is a good barrier to this virus but transmission risk goes up with open sores and such breaks in skin.
HPV has the potential to cause cancer, even in men, although this is less common than in women. Getting vaccinated (Gardisil or Silgard), even for men, is a consideration. In the future HPV-related genital cancer will be much less common, although common warts will still be a nuisance. The occasional wart is trivial, you can freeze it off yourself with a kit from the pharmacy. An outbreak of warts is more challenging.
Herpes is a bigger nuisance, first episode can be very painful to asymptomatic, and episodes of pain associated with outbreaks usually diminish in frequency and intensity over the years. Genital herpes does not cause cancer or any other debilitating systemic diseases.
If you know you don't have herpes, the only official recommendation is to use condoms, and keep your fingers crossed. In theory, taking valacyclovir on a daily basis would reduce the risk of contracting infection further, but this is unproven, is not official policy and would be very expensive.
If you know you have herpes, well, let your conscience be your guide. Official policy: the socially-responsible thing to do is for you to tell the person you are going to have sex with that you are infected, an awkward moment at best. To protect women, the combination of condoms and daily valacyclovir (which reduces asymptomatic viral shedding) reduces the risk of transmission to 0.60 per 1000 sexual contacts; if the man uses condoms alone, her risk is 1.27 per 1000 sexual contacts.
An afflicted female SP, insisting on condom usage, has a transmission rate to men of 0.35 per 1000 sexual contacts. If she takes daily valacyclovir and also insists on condoms, the risk goes down to 0.23 per 1000 sexual contacts
