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SameTime
If your company uses SameTime you can use the instant messaging program Pidgin (formerly known as GAIM) with the plugin “Meanwhile”. On Debian (and AFAIK Ubuntu) this is apt-gettable. Meanwhile makes it possible to connect to a Sametime server and it works like a charm 
Since GAIM 2 it is integrated in Pidgin/GAIM, in Debian just install “libmeanwhile1”.
There also is a native Sametime-Client since version 7.5. As an advantage you get any function which happens to be in Sametime. The drawback is that it's quite slow (especially compared with Pidgin) but otherwise it works really fine (especially since version 7.5.1). In notes 8 this version is integrated and I recommend running that if you use Notes 8 anyway.
User Preferences
One thing that really irritates me and I haven't found a solution for so far is the loction of the user configuration.
notes 8 stores its configuration in ~/lotus whereas SameTime 8 stores its configuration in ~/Lotus. If you know that filenames are case-sensitive in Linux/UNIX you can see the problem…
I haven't found any way at all to change that path in SameTime. So if you know of a way please let me know! Using the integrated SameTime client in Notes is not an option for me, I prefer to run Notes and SameTime independently.
In Notes you can edit the notes.ini and tell the launcher to use an ini in a different path, but still the ~/lotus directory with some icons in it will be created.
Furthermore, SameTime creates (or used to create?) a file called able.preferences in your home directory.
As I like my home directory to be clean, I wonder if IBM has ever heard of dotfiles and -directories?!?