Will general non-standard transactions ever be allowed? To the best of my knowledge, currently "Satoshi" client relays and most pools accept only standard (transfer or generation) transactions. Besides, community is working on M-of-N transaction type. Adding non-standard transaction to the blockchain is nowadays pretty problematic.

While currently enabling arbitrary scripts in transactions could be disastrous due to possible bugs in code (or in the script system itself), I wonder if it is planned to allow arbitrary transactions somewhere in the future, or will most of the network always be restricted to some set of "good" transaction templates?
The current development direction (January 2013) is to tighten up the IsStandard() checks even more. For example, we would like all signatures to conform to a very strict, canonical encoding to make life more difficult for potential attackers. 

Allowing more opcodes or opcode patterns (or all opcodes/patterns) to be considered IsStandard() is certainly possible; before doing that I'd like to see a thorough analysis of the possibility for mischief using the current set of opcodes  and a lot of prototyping on the test network (where the IsStandard() check already allows all enabled opcodes).