The answer depends on multiple factors. These factors include: what type of ring game you are playing, the preflop raiser's statistics, and your position.
In a standard 6 max game with a lot of regulars, I think the best option with small PP's when facing a raise out of position is to 3 bet, for a few reasons. First, these hands play very poorly OOP and most of the time you just flat the raise you will either be folding the flop or having to make very tough decisions on later streets which could cost u lots of $$. And second, the raising range of a standard regular in today's 6 max and full ring games are fairly wide, and they won't be able to call your 3bet without a good hand. I find that my 3b's with small PPs usually just take the pot right then and there.
That being said, set mining can be extremely profitable. I like to set mine with a greater frequency when there are already multiple people involved in the pot (a raise and a call or two ahead of me). I will still set mine OOP sometimes even against just a single raiser..I'm not 3 betting these hands with 100% frequency. Knowing the percentage of hands your opponents are raising from each position will help you determine what you should do. If my opponent is in the cutoff or on the button and is raising something like 75% from these positions, it becomes an easy 3 bet for us with a small PP. Keep in mind that you will need to make good decisions and c bet a lot of boards with one over when he defends your 3 bet.
Most of this info holds true in full ring games as well. Use position and opponent statistics to help you make good decisions preflop. Just flatting small PP's OOP every time is definitely -EV.