Just a quick guide to patching a standalone ESX 3.5 Server using esxupdate from the service console:

Download all available patches to your local computer from the following link: (ALSO DOWNLOAD THE FILE CALLED contents.zip)

VMWare Patch Download Page

Decide where to place the patches in a partition with enough space to accommodate the patches on the target ESX Server. It is not recommended to use the root ( / ) partition at all. A good strategy is to create a directory called updates under the /var partition.