All recommended applications and utilities are free of charge. Most are open source.
Recommended Cross Platform Programs and Utilities (meaning they work on Windows, MAC, and *nix)
Browser
Firefox We highly recommend Firefox with NoScript and AdBlockPlus extensions.
Email
Thunderbird with Penelope (Eudora 8.0) Thunderbird with Penelope (the Eudora Interface and features) is a great fit with Cotse.Net services. It is Open Source, free, and extremely robust. It also provides the privacy and security you require.
Email encryption
Gnupg Encrypt your messages and files with the best and highest rated encryption so that only you and your receiver can read, reply, or open. Also digitally sign text to prove it was from you.
Email encryption made easy
Enigmail Integrates gnupg encryption and signing into Thunderbird, Eudora, Mozilla, and SeaMonkey clients. Automatic encrypt/decrypt/sign/verify e-mail. Eudora 8.07b users should download Enigmail for SeaMonkey 2.0.
Encrypt entire drives.
TrueCrypt Open Source Disk Encryption. Create virtual encrypted storage containers that can be mounted as a disk, encrypt USB flash drives and other USB devices, and it will even encrypt partition where OS is installed for boot auth prior to launch.
Windows Recommended Utilities
Gnupg Encryption Utilities
GpgOL Outlook extension to add gnupg to Outlook similar to how Enigmail adds it to Thunderbird/Eudora.       Gpgee Adds GPG functions to Explorer shell allowing right click to encrypt or sign files.         WinPT Although no longer being developed this still works to add the ability to to encrypt/decrypt/sign/verify clipboard contents as well as text in open windows. Does work with Windows 7 but you must right click and copy rather than using CTRL-C for it to see text in the clipboard.
Firewall
Comodo The best free firewall, advanced.
Remove deleted files and wipe slack space.
Eraser Open Source. Far better rated than any of the overly-hyped "eliminators". Free.
Detect and remove spyware.
SpyBot One of the must have's for spyware detection and removal.         AdAware The other must have for adware and spyware detection and removal. Free.
Detect and remove viruses.
AVG A good antivirus free for home use.         Avast Another good antivirus for home use. Run with AVG.         Microsoft Security Essentials It gets good reviews and catches things the above two miss, but read below before using, it was a toss-up as to whether or not we were going to include this here. Note: Microsoft Security Essentials forces membership in MS Spynet, an "online community dedicated to reporting and stopping malware", or rather, everyone else running this. Basic membership in Spynet means reports are sent to MS by MSE. Reports could include a list of running processes, installed programs, and information on the files identified as malware and the action taken. Not very privacy concious, but quite frankly, MS has access to all this anyway, so if you are trying to keep your Windows computer a secret from Microsoft, good luck.
Useful System Utilities
Autoruns Control everything that is automatically started         Process Monitor  Monitor processes and what they are doing, stack calls, dll calls, network calls, and more         Process Explorer  Explore your currently running processes as well as previously launched processes         TCPView  List all network listening applications
MAC only utilities
We could use suggestions