The other way is to enable the URL handler in Phoner (Options/Web). Then you can generate links like phoner://0123456789
I hope this helps.

PhonerLite supports "callto:" and "sip:".
Phoner is more suited for ISDN/CAPI. PhonerLite is the VoiP specialized version of Phoner.

Such URL handler is just a registry entry. You can add "tel:" manually. PhonerLite should work with it.

Just discovered it is possible to define custom URI and map it to specific application. It require registry edit but for intranet application with limited number of users/computers it is far enough. Create registry entry:

REGEDIT4

[HKEY_CLASSES_ROOT\Phoner]
@="URL:phoner Protocol"
"URL Protocol"=""

[HKEY_CLASSES_ROOT\Phoner\DefaultIcon]
@="\"C:\\Program Files (x86)\\Phoner\\phoner.exe\""

[HKEY_CLASSES_ROOT\Phoner\shell]

[HKEY_CLASSES_ROOT\Phoner\shell\open]

[HKEY_CLASSES_ROOT\Phoner\shell\open\command]
@="\"C:\\Program Files (x86)\\Phoner\\phoner.exe\" \"CONNECT %1\""

If you need to start phoner case by case with different outgoing phone number, just install Phoner in multiple directories, set up each install with custom settings and create each URI protocol for each phoner install. Than create <a href="phoner://123456789">123456789</a> style links in your web app. By click on such link, phoner will be started and given number is dialed.