I was uploading a big file (iso of +/- 6 Gb) and somewhere in the middle I've got an I/O error. Now I can't see the file in the datastore and I lost +/- 3 Gb.
How can I delete the 'partial' file or reclaim the space?
Depending on the way you view the datastore you may or may not be able to see the file. I've noted that the ESX VI client's datastore viewer does not show some files. If you were to ssh into the system and cd to the VM folder on the datastore (cd /vmfs/volumes/datastore_name/vm_name/) then you should be able to see the file, it may have a .part extension. (ls -la shows all files)
To enable sshd on ESXi see this article: http://www.yellow-bricks.com/2008/08/10/howto-esxi-and-ssh/