I was doing some missions for mr. House when I got some mission from the NCR and the legion which said if I continue to work with mr. House I can't do missions for them. I also notice a mission from the Legion that said to kill Mr. House. Which one should I choose? Yes man, Mr. House, NCR, or the Legion?

That's entirely up to you. Who's jib do you like the cut of most?

Its entirely up to you. Each has it's advantages and disadvantages. It all depends on how you want to play the game.

What are the advantages and disadvantages of all the factions?

They all let you win with them. NCR has the most quests to do all over, so it's a lot easier to get loved by them quicker, but other than that, there isn't really any advantage or disadvantage to choosing any of the factions. Just different primary quests to follow for each one, towards the same eventual goal.

Well if you want more combat then go for Legion, if you want more quests then go for NCR, if you want more options with minor factions then go with Yes Man and if you want to help a computer screen then help House.

Just talk with each of the leaders of all the above menchened factions
Ambassador Crocker (NCR) Caesar (Legion) Mr House (House)
or if you don't like any of them side with Yes Man

Its all up to you...Do you like America(NCR) Do you like Rome(Ceasers legion). Do you like the Lucky 38 in its self(Mr.house). Dont like any(Yes man)

I would personally side with NCR.

My suggestion would be to go by your own personality. If you are very patriotic i would go NCR. If you have always dreamed to rule the world I would go Yes Man/Independent. If you enjoy being the man behind the mask I would suggest Mr. House. And if you are pure evil and hate society I would go with the Legion. I played using every faction and enjoyed all the endings