I solved this issue by adding another application.cfc in the mobile directory:
<cfcomponent extends="intranet.Application">
<cfset this.name="mobile" >
<cffunction name = "onApplicationStart">
<cfset super.onApplicationStart()>
</cffunction>
<cffunction name="onRequestStart">
<cfset super.onRequestStart()>
</cffunction>
</cfcomponent>
Then, I just check if the user is on the mobile site or not with:
<cfif application.applicationname EQ 'mobile'>
do something
<cfelse>
do something else
</cfif>
Thanks for the help