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PuTTY's SSH-2 host key selection policy for new hosts currently involves a fixed preference order of RSA then DSA. I occasionally think it would be good to add a preference list to tweak the policy, either to put DSA first (if you're really mad) or to move DSA to below the "warn below this line" line.
When a new host key prompt is given, PuTTY should mention if it already has host keys for a host in other formats - particularly important when the default protocol changes to SSH-2.
Update, March 2016: we've finally implemented a preference list. We also sometimes list better algorithms in the host key prompt, but only in the specific case where we're using an algorithm below the "warn below this line" line due to hostkey-prefer-cached.
(We still don't mention SSH-1 keys when showing an SSH-2 key prompt. SSH-2 became the default over a decade ago, so that ship has sailed.)