It doesn’t matter if you wanna use un-encrypted Instant Messenger such as Yahoo Messenger or other popular messenger services. But, you might want to try an Encrypted Instant Messaging Service called as BitWise IM. You can use it for free if you choose for home or personal use. BitWise IM also available for Business or corporate. Features in BitWise are: File Transfer, Voice Chat, Text IM, and more
Download: BitWise IM
License: Free for Personal / Home
Website: www.bitwiseim.com
Compatible: Windows, Linux, Mac OS X
PS: Image taken from: http://image.wareseeker.com/software/Communications/Chat-Instant-Messaging/details_bitwise-im-for-linux-1.7.3.png

If you looking for an Instant Messenger client that has ability to make Text Chat, File Transfer and Remote Desktop securely with Free License (under GPL License) you can try to use CSpace. It works for Windows and Linux
Here are some of the salient points regarding the CSpace architecture:

User Identity

All users create 2048-bit RSA keys for themselves.
A user is uniquely identified by his RSA public key.
Every user has a contact list, which is just a list of public keys known to that user.
A user assigns names to the public keys …

If you want to store any history archive or history from your Instant Message that came from Pidgin, digsby, Miranda, ICQ, Yahoo Messenger, Windows Live Messenger, ichat, MSN, QIP, Centericq, Adium, Fire, Climm, ysmICQ, Ayttm, Licq, Sim-IM, MIP iM, mChat, gsICQ, Jimm, and more in the web server aka web base, you should try Simlk.

Simkl automatically saves all of your important IM conversations on a secured web server, the same way you save your e-mails. And more importantly software installation is only needed for Windows Live Messenger. There is no …