Can I exit Thailand to Cambodia to get another 90-day stamp on my Non-Immigrant O visa without affecting my future visa applications?

Well if you're on a year-long multi-entry Non-O visa from a thai consulate you've HAD to bounce out and back every 90 days because that visa only gets you a 90 day entry stamp.

Doesn't matter where you bounce out and back on it and it isn't gonna affect you getting another visa in the slightest. In fact most people get 15 months out of the visa and then another 2 months on the 60 day visit thai family extension tagged to the end of that last 90 day entry before they have to slog back to buy a new one

BUT

a word of caution if you're thinking of bouncing yourself out and back at Cambodia DO NOT use Aranyaprathet/Poipet as the crossing.

You might as well get the most you can get out of the visa.