As a player inclined to argue with the GM when I feel the GM is making a bad call, I try to keep several things in mind:
Is this issue big enough to matter but small enough to win?
This may seem obvious, but a lot of people, both players and GMs, seem to forget it.
Is this a clear cut rule in the RAW, or is it one of the gray areas?
If something is clear in the RAW and not covered by an existing house rule, I feel it should be played RAW. If it is not, especially if it is a matter of interacting rules from different books, I will usually let it drop after explaining my interpretation. Of course, usually I will discuss things like that with the GM ahead of time...
This leads to etiquette:
Be polite!
I still sometimes forget this rule...
Talk to the GM ahead of time.
If I am planning on doing something that is in the gray areas with a character as part of their build, I will talk to the GM about it outside of the game ahead of time.
If time allows, look up the rule before interrupting the game.
It doesn't usually take more then 30 seconds or so to look up a rule, and if it does, it probably isn't as clear cut as I may think it is. I have been saved the embarassment of arguing when I was wrong by this one. Granted, combat tends to cause most of the problems here.
Know when to let go.
Self explanitory, but hard to remember in the heat of the moment. No game is worth even a 5-minute heated argument on the rules.
Suggestions I would make to GMs:
Spell out what kind of game you want ahead of time.
Many arguments could be prevented if rules-oriented players were informed ahead of time that the rules would be bent or broken for the sake of the story.
If the rules aren't clear, but the player has a reasonable argument, rule in the player's favor. It generates goodwill and trust from the players and helps diffuse GM vs. Players attitudes. You can always find firmer footing after the game and explain it to the players when nothing is on the line. This goes double for the small stuff.
If you haven't spelled out a change to RAW with a house rule before the game, don't implement one on the fly. Few things annoy players more then to be told something won't work because the GM doesn't like it. It is a game. Games have rules. It isn't unreasonable to a player to expect to be able to know the rules when the game starts. In the Blink example, if I were playing an arcane caster, I would be expect the GM to 'spell' out any changes from the RAW ahead of time.
Consider how a rules call will look from the other side of the screen. If something could be perceived as favoritism, you should seriously reconsider the call.
Be consistant.
Obviously, some arguments happen because the player or GM is an power-hungry jerk with no social skills, but in that case, arguments over the rules isn't the real problem.