Under what conditions would a helicopter be allowed to fly at low altitude over populated areas?
I have no idea about the specific flight you saw, but the general answer to your question about operating legally below the minimum safe altitudes in 14 CFR 91.119 is that the FAA can grant a waiver allowing lower flight. The waiver process says that to get a waiver to 91.119(b) (flight over congested areas) there must be a public interest reason but aircraft can't be lower than 500ft unless lives are at stake:


  When issuing the waiver, the altitude requested should be an absolute
  minimum, but may not be less than 500 feet from persons or property,
  unless necessary to safeguard human life


There isn't enough information about the helicopter you saw to say what was going on but assuming that it really was a Chinook at at 100' AGL then it was too low even for a waiver, according to the FAA's process. But the most obvious explanation is simply that it was taking off; helicopters take off in a range of attitudes and airspeeds and some of those takeoffs are probably relatively low and fast. It might have been a medevac flight (they're often brightly painted) or perhaps something to do with logistics or construction; if you got the N number then you could look it up.