For ESXi 4.0 and below, patching can be done with vSphere Host Update Utility.
For ESXi 4.1, vSphere Host Update Utility is no longer supported. Patch using command line:
1) Download patch bundles from VMware's support website: www.vmware.com/patch/download/
2) Upload the patch bundles to your datastore. (You can use vSphere client to do this.)
3) Put the ESXi host into maintenance mode.
4) SSH into the ESXi box. This blog shows how to enable SSH on ESXi 4.1.
5) CD to the datastore and use esxupdate --bundle to patch ESXi:
esxupdate --bundle ./ESXi410-201011001.zip update