Links like mailto:firstname.lastname@example.org 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
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