I think the attack on CBC that you're referring to is a known-plaintext attack where an attacker can manipulate a plaintext by adjusting the previous block of ciphertext. But this same sort of attack also applies to CTR.
 I misinterpreted the OP's referenced to a CBC attack. The one I describe here allows intelligently modifying plaintext by modifying the ciphertext. This is a valid attack to be concerned about and applies to both CBC and CTR, so I will leave it as a part of the analysis of the modes of operation, but it is not the attack mentioned by the OP. [/edit]
CTR is a good mode overall, but it must be used in the right context given that it is a stream cipher. You should not use it in a case where you will be re-encrypting the same data with the same key and IV (for example if you're doing disk encryption). In practice, this often means that you should only use it if you're willing to completely re-encrypt data every time it's edited/saved/transmitted.
The newer block mode XTS is an interesting mode because it does away with the ability to modify the plaintext by altering the ciphertext (like mentioned above), and it also allows for single-block encrypt/decrypt access like ECB and CTR. The disadvantage to it is that it has the same information leakage that ECB and CTR have, namely editing/re-saving ciphertext leaks exactly which blocks were modified. In practice, however, I don't think many people are concerned by that.
Right now there is no official "best" mode, but it seems like there is a heavy favoring of XTS due to the fact that plaintext is not malleable and that it is well-suited for many uses, both of CBC's and CTR's domains. Disk encryption products have switched en masse to XTS recently. I don't think network communications has, though.
For what it's worth, in the book Practical Cryptography (first edition) by Niels Ferguson and Bruce Schneier they made a comment that CTR was "their personal favorite" (paraphrased quote) mode of operation at the time. That was written in about '03, though, and I don't know if that comment was preserved for the second edition of the book; it was made long before XTS came around.