Hey, I am going to replace the door trim. What is the best way do this. Would it be easier to take the door of then put it on? Should I put glue on the door or the rubber first?

Are you referring to weatherstripping?
Scott

If you are refering to replacing the weatherstrip, you do not need to remove the door. The weatherstrip will go on fine.
You need to use the right type of weatherstrip adhesive, 3M yellow, or black. You should apply the glue to both the door, and the weatherstrip, and let them set up for a few minutes before installing.
Make sure you have all of the old gunk off of the door first, tho, or the new stuff will not stick very well.

clean,clean,clean and once you get it in place a few well placed strips of masking tape works wonders

I did mine this past weekend using the 3M yellow adhesive. It is very important to remove all of the old adhesive. 3M also makes an adhesive remover which I also used. It worked well as did the masking tape. No need to use large gobs of the adhesive. As Joel stated above, apply the adhesive to both the door and new rubber. Let the adhesive "skim up" a few minutes then begin to route the new rubber holding in place with the masking tape as you go. Keep your beads of adhesive near the center of the new rubber. This will minimize the squeeze out and reduce the mess. Taking your time while applying the adhesive will save a lot of clean later.
Good Luck,
Scott