What?

Password Management:
LastPass: http://lastpass.com
KeepassX: http://www.keepassx.org/

Encryption:
Luks: Built into most distros and allows you to encrypt files mounted via loopback or whole disks. Gnome Disk Utility will use this to create encrypted disks.
Truecrypt: http://www.truecrypt.org (Realcrypt for people on Fedora using RPMFusion)

Video editing/Transcoding:
Handbrake: http://handbrake.fr/ (Note: The daily releases are better for modern distros)
AviDemux: http://fixounet.free.fr/avidemux/ Basic editor that I use to rip out commercials from my TiVo movies

Media Players:
Totem
VLC
Rythmbox

Bittorrent:
Transmission

iPod/iPhone/iPad Management:
gtkpod
Rythmbox

eBook Management
Calibre

TiVo Management:
Kmttg: http://code.google.com/p/kmttg/ Great tool to pull movies off my TiVo and transcode them. Can be setup to automatically pull certain shows, transcode them etc…
pyTiVo

Web Browsers:
Firefox
Google Chrome/Chromium

Video Conferencing/VOIP:
Ekiga
Skype

HTML Editing:
Komposer

Instant Messaging:
Empathy

Remote Control:
VNC
NXClient/NXServer: www.nomachine.com

Backups: I previously used Deja-Dup but wound up spending the money on SpiderOak because of the zero-knowledge encryption and the advantage of a cloud based solution
Deja-Dup: https://launchpad.net/deja-dup
SpiderOak: https://spideroak.com/

Office Apps:
OpenOffice

Disk Recording:
Brasero: Part of almost every Gnome distribution by default as the recording software

Virtualization:
KVM
VMWare Player
VirtualBox

Blackberry:
Barry: http://netdirect.ca/software/packages/barry
Bluetooth Tethering via Network Manager

Email:
Thunderbird

Newsgroups:
lottaNZB: http://www.lottanzb.org/
PAN: http://pan.rebelbase.com

I have been testing a Blackberry 8800 for work and installed the GMAIL client. This was the message I received:

For anyone who can’t see it the message is:
The application gm_8700_v4_0_L1 is attempting to access phone logs. Would you like to allow access?

A couple of notes:
1) Google detected this phone as an 8700 but the application works fine.
2) GMAIL seems to function properly if I click no.

So my questions are:
1) Why does Google want or need access to my phone logs?
2) Has it always done this and I only recently found out due to my 8800 prompting me?

To say the least this makes me very nervous and so far the only purpose I can see for this is to allow me to dial a number from inside an email but why wouldn’t it ask me when I attempted to dial rather than after I open the application?

Update: Searching through the settings shows no option to disable this.