I use Isopropyl Alcohol in the stem and shank after every bowl, but not in the bowl itself other than what gets on the draft hole. Lots of people only sterilise periodically or when they start to smell something.
Isopropyl is perfectly safe in trace amounts (thus used for sterilising skin) and leaves no residue or smell after it evaporates.
Apparently some places add other things to their rubbing alcohol though, so it's probably good to check whether or not your local supply is a pure Isopropyl/water mix.
Ironically I've read that 70% is actually more effective at disinfecting because water is necessary in order for bacteria to absorb the alcohol, so the 99% stuff isn't necessarily "better", though I still prefer it because I assume I'm dissolving oils as much as killing bugs.
If you have a cheap supply of Everclear that's certainly not a bad option either. The only problem with regular high proof alcohol is I assume it will add a smell to the pipe, and of course it's probably more expensive.