The best replacement for kayako is zendesk.

The best alternatives to kayako are rated as following:
★★★★★  zendesk
★★★★★  samara
★★★★  whmcs
★★★★  sadako
★★★  freshdesk
★★  otrs
★★  osticket
★★  smartertrack
★★  desk.com
★  cerberus
★  vision helpdesk
★  supporttrio
  deskpro
  sysaid

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

Other search terms related to kayako and their ratings are:
★★★★★ whmcs
You have in mind a companion for kayako and it is not yet here? Propose!



Google Trends

Scale is based on the average worldwide traffic of kayako in all years. Click on graph for more.
kayako
zendesk
samara