1. Multi-factor auth for the Linode Manager.
Simple user name/password authentication just isn't adequate when we're talking about a portal that gives complete control to a customer's entire virtual infrastructure. Any provider can be hacked. When it happens, it should be more difficult for the hacker to gain access than simply having to crack passwords. Amazon Web Services has a very nice and easy-to-use setup via Google Authenticator. Please take a look at it.
2. NodeBalancer Private IPs or IPv6 to Back-end Nodes
I need to load-balance database reads over the private no-fee network.
3. Named Snapshots
A simple thing that would make my life easier.
4. Clone API
Oh wait, you added that! Almost 11 months to the day since I first requested it, but better late than never!

And thanks for asking. It's nice to know you are listening.