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From the OpenSSH 5.4 changelog:
* Passphrase-protected SSH protocol 2 private keys are now protected with AES-128 instead of 3DES. This applied to newly-generated keys as well as keys that are reencrypted (e.g. by changing their passphrase).
PuTTYgen should certainly learn to import such keys. It should probably also have the option to export keys encrypted with either cipher. SGT, 2010-04-12: r8917 can now import the new keys, but won't export them yet.
Audit trail for this wish.