Now to answer your question, with 50% less idealistic ranting!

There is definitely a canon of "safe" extensions in the community.  Hierarchical libraries (that's not even an -X flag, it's just on), multiparam typeclasses, fundeps are among them.  I can't say whether FlexibleContexts is.

However, your question is rather moot here, as you are using the mtl.  It uses UndecidableInstances, whose blessing into the de facto standard would require as a precondition the batshit-insanity of the de facto community.

I personally use transformers as my monad library, as it is (as far as I know) the only Haskell 98 monad library on Hackage (you'll hardly notice the more explicit lifts, I promise!).  However, looking a bit more optimistically into the future, I'd say mmtl is the "most likely to succeed", since it solves the combinatorical explosion problem which haunts all the other monad libraries (and at least avoids the extensions which are doomed to failure). 

Anyway, it is never too early to free yourself of mtl.  Look at the monad libraries on hackage and weigh their pros and cons; the only thing special about mtl is its mediocrity. 

Luke