Watashi is safe and proper, although totally gender-neutral and might be perceived as being more "pansy"-like than boku.
Ore is less socially acceptable and demonstrates a certain over-confidence (or social ineptitude) that indirectly sets a character up to be perceived a certain way. This can be both good and bad, of course. Some characters (and real people too even more so) switch to another pronoun when formality demands it, reserving their use of ore for casual situations with friends and family.
Boku feels a bit like a compromise; it gives a sense of individuality/masculinity for a male without stepping on anyone's toes. This is typically what I myself use, although as a foreign speaker of the language I switch to "watashi" if I feel I don't know a person very well. That might just be excessive cautiousness on my part, however.
Other pronouns, well...there really aren't many options you'll see for male protagonist-types. lol. Ware is way too archaic and rude (maybe if Walhart from Fire Emblem 13 was a protag), washi'd fit if the VN took place in a retirement home, and the others are either blatantly feminine, regional or extremely bizarre to see in day-to-day life.