The best replacement for clickonce is installshield.

The best alternatives to clickonce are rated as following:
★★★★★  installshield
★★★★  xbap
★★★★  windows installer
★★★  java web start
★★★  wyupdate
★  updater application block
★  installer

Your alternative for clickonce is not listed? Suggest!
Speaking about clickonce, one probably shouldn't forget about msbuild.

Other search terms related to clickonce and their ratings are:
★★★★★ msbuild
★ vsto
windows installer
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clickonce
installshield
xbap