Once you've created Ubuntu instance (I've used ubuntu-9.04-jaunty-base-64 image), it's not really trivial to login. Below are the steps.
1. You have probably already created key pair on Amazon. If you didn't - go to Amazon AWS management console, (https://console.aws.amazon.com/ec2/home), and create a new key pair.
2. Putty doesn't accept this key as it is, it needs to be converted to a format useable by Putty. Using PuttyGen (puttygen.exe), do this:
Conversions -> Import key -> import key you've got from amazon (pem file) -> Save private key.
3. Open Putty, in host name enter public DNS name for the Ubuntu instance.
3.1. Go to SSH -> Auth, and choose key you've created in "Private key file for authentication" field. Click Open.
4. In "login as" prompt enter "root".
Done.
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