Using actual company logos in movies/animations vs. fake ones, do's and don'ts.

You pay, you play.

By the time 2001 came around, most of the companies mentioned in 2001 A Space Odyssey were out of business. That kind of thing makes a movie unintentionally funny.
And @seazen is right. They have to pay to display copyrighted symbols.

Here’s a short movie that answers the question pretty brilliantly.

you would think the companies would appreciate the free advertising.or not. I always wondered what kind of deal was made in the movie “Enemy Mine” with Louis Gossett Jr. A lone space traveler is lost and alone on a planet and suddenly finds a Pepsi can in the dirt.

Its all about the advertising dollars. If you want visibility in a movie, you pay for it. Either in dollars or credits. It is also can be a royalty issue.
Kill all the lawyers.

I think you need permission to use a logo or something, unless it’s a critique or satire. I doubt Nestle agreed to this video for example: http://www.youtube.com/watch?v=1BCA8dQfGi0