I was planning on upgrading from ESXi 4.1 to 4.1 update 3 using update manager. If I run into issues, can I still open a support ticket (my support is valid until 2016) or will they just assist me with an upgrade to 5.x?
Yes you can still open tickets
Now is technical guidance phrase
Technical Guidance Phase
Technical Guidance, if available, is provided from the end of the General Support phase and lasts for a fixed duration. Technical Guidance is available primarily through the self-help portal and telephone support is not provided. Customers can also open a support request online to receive support and workarounds for non-business critical issues on supported configurations only. During the Technical Guidance phase, VMware does not offer new hardware support, server/client/guest OS updates, new security patches or bug fixes unless otherwise noted. This phase is intended for usage by customers operating in stable environments with systems that are operating under reasonably stable loads.