Which one of the Block Cipher modes is the best?
Personally I like the modes that support integrity checking and authentication, e.g. GCM, as they only require one key, and are not vulnerable to changes in the cipher text. One particular important problem area is padding oracle attacks, which are much more common than people seem to admit.

Note that GCM/AES is - just like CTR - a block cipher in stream cipher mode; Basically GCM consists of a GMAC and CTR combination. 

GCM is supported by XML encryption v1.1 (XML encryption by itself is very vulnerable to padding oracle attacks). There is also http://tools.ietf.org/html/rfc5288 which describes the use in TLS and http://tools.ietf.org/html/rfc5084 which describes the use in CMS.

GCM seems to have some support, e.g. Java 8 introduces GCM in the standard Java Runtime. For Java 7 and below it is required to use an external provider such as Bouncy Castle.