You're not going to get hepatitis or HIV or swine flu through your shoes.

You've basically only got two things to worry about, wart viruses and athlete's foot fungi.

Here's what the CDC says generally about disinfection. (Note that alcohol is not effective against non-enveloped viruses like HPV; soaking for 10 minutes in a 1% bleach solution is broadest spectrum but probably hardest on the shoes; 3% peroxide is good against viruses and "fair" against fungi.)

But it's not all that easy to re-infect yourself with either plantar warts or athlete's foot from your own shoes, so I doubt if someone else's shoes would be different. If it were me and the shoes appeared clean, I'd give them a wipe with a weak bleach solution, maybe replace the insoles, and wouldn't worry about it any more.