It depends on the game, the severity of the imbalance and the circumstances of why you are playing. Noob toobing can be pretty annoying, but 9 times out of 10, if somebody is actively trying to go after the noob toober, they will either kill him or he will be forced to switch to an actual gun.
I was playing soul calibur 4 a while back with a friend. I was playing nightmare and beating her down pretty mercilessly when she was on the ground, while she was citing some tournament rule saying that I wasn't allowed hitting her while her character was on the ground. I found it pretty irritating because it wasn't a tournament game and she was better than me at the game by a wide margin and would win most of the matches anyway.
Another time (many years ago), I was playing Halo 2 with a group of 8 friends, and the two players who actually played online were abusing all kinds of glitches (jumping outside of the level, using 'invisible stair cases' using these weird glitch jumps) to beat the shit out of us! THAT is something I'd consider to be unfair.
In online random match ups, anything goes, because it is impossible to agree on what you are and are not allowed to use beforehand and everyone (usually) has access to the same abusive weapons and bonuses. Glitches are never alright though, and should be reported if possible.
In casual games in with friends, if you want to make special arbitrary rules, everyone should agree on them beforehand (no citing tournament rules to somebody with no knowledge of them when you didn't notify the other player(s) that you want to play by a special ruleset). If there is something truly game-breaking that everyone can agree not to use, then that will make the game more fun for everyone.
In tournament games, the people making the rules will have enough knowledge of the game (often more knowledge than the developers themselves) that whatever rule modifications they make will probably have been necessary to make the tournament fair. Sometimes there will just be some combination of weapons, attacks, bonuses or whatever that just cannot be countered and a tournament where people only use this tactic would be boring.