A recent newsletter article from Darren Alf of Bicycle Touring Pro posed this question as a controversial debate.  I admit to not having read the article in its entirety as I have my own ideas about this topic based on personal experience.

This contributes nicely to another post regarding the differences between bicycles for touring and bicycles for commuting.  One of the comments I hear time and again concerning the attributes of a bike specifically designed for touring is that they often ride and handle "better" with loaded panniers.  For someone who has experienced such an exquisitely designed bike their only reason for considering a trailer would be to carry more stuff or with regards to commuting or utility use, awkward items that simply do not fit on a bike very well.  I use our bike trailer most routinely to haul a seven gallon water container and it works really well for that.  In my mind there is no debate. When a person enjoys riding a particular bike so much that they want to use it for touring that bike may not ride as well with a load, therefore implementing a bike trailer is a natural choice.  

Some conveniences of a trailer should be discussed. Smaller, lighter weight panniers can be used on the bike to reduce wind resistance with a nicely packed trailer and its' low center of gravity. It is a method of weight distribution that many folks find appealing.  Another nicety is ability to simply park the trailer at one's campsite and be able to explore trails, run errands without having to take the time to unload a lot of gear.  Reducing the weight on some bikes also reduces maintenance tasks of wheel truing, spoke repairs or potential frame damage. This could lead to another discussion of frame materials and ease of repair, ie steel being easier to weld than aluminum.  

I prefer not to haul a trailer for rugged mountain bike treks.  For that I prefer a front rack on a mountain bike which I also use for commuting.  It is much less cumbersome and for mountain bike touring and trail riding, ability to maneuver over and around rocks, trees and other hazards where a trailer can be a burdensome nuisance, it just depends on the terrain. 

That having been said, we are not discussing bike travel here in the sense of hopping on planes or trains, obviously a trailer would prove to be not only a burdensome nuisance, but may not be possible depending upon the circumstance. In which case a folding bike used with a trailer could possibly work out just fine for packing and transporting.  

There, that wasn't so bad, some things to consider for your own packing options on your bike travels whether they be touring or commuting panniers or a bike trailer both have their place.  That's why I keep both around depending on what my needs are, at least I know they're being met.  If there's one thing I have learned from a bike trailer it's that you can take what you want from your past and put it all behind you.  Since I received a shiny new Minoura MT 4000SF steel front bike rack for Christmas I'm excited about all I have to look forward to. 
Cheers.

Links related to this topic:
Top Four Trailers for Touring and Commuting
Affordable Quality Bike Trailer
Quintessential Touring Bike VS Bike Packing
Pack Kit List for Multi Day Touring