I've been to Japan twice now and have spent a good deal of time drinking in Tokyo. I've never had any issues.
Hostess bars have a reputation for this kind of behaviour (i've never been to one so i can't speak to the truth of that reputation).
I've never had any issues with drink spiking or credit card fraud, even when i've been drinking alone in Roppongi.
You don't really need to take any special precautions apart from the obvious:
- Steer clear from bars that are empty.
- Don't go drinking on your own
- Stick to bars frequented by gaijin
- Avoid the hostess bars (I'd suggest this anyway. Between door fees and drinks costs you're looking at an expensive night)
- Keep an eye out for sit down charges (we got stung with this once, a bar in shibuya charged 4 of us almost 9000 yen for 4 drinks)
If you're going drinking in Roppongi (Tokyo), the Heartland bar in Roppongi Hills is a good place to start out the night.
Generally though Japan is incredibly safe for drinking in. You're at much higher risk drinking in somewhere like London or LA than you would be in Tokyo