Links like mailto:name@company.com are not automatically handled by Lotus Notes in Ubuntu after it is installed.
The solution is simple:
1) Go to System->Preferences->Preferred Application
2) In section Mail Reader, choose Custom
3) Enter this command in
/opt/ibm/lotus/notes/notes %s
4) Do NOT choose Run in terminal
An alternative to this is to set Firefox to directly handle mailto-links:
Go to Edit->Preferences->Applications (Tab) -> Set mailto to /opt/ibm/lotus/notes/notes