Another Linux fan here...
Check out these sites...http://radio.linux.org.au/http://www.ibiblio.org/pub/Linux/docs/HOWTO/other-formats/html_single/AX25-HOWTO.htmlhttp://he.fi/archive/linux-hams/about.htmlhttp://www.qsl.net/kf8gr/index.html
For CW practice, I use a non-graphical command line package named, appropriately enough, 'cw', which is an installable package in the distribution I use (Gentoo) or available from http://cwrapper.sourceforge.net/
I wrote a quick and dirty bash script to input random characters to it, with command line arguments for speed, tone, number of characters; and echo the characters once completed.
Other packages include...http://cwtext.sourceforge.net/http://www.qsl.net/pg4i/linux/cwdaemon.html
and I'm sure there are many others... do some internet searching.
There are Linux-based logging programs around (check the links on the various sites, above), but haven't used them, because (gosh, do I admit this in writing!?!..) but I still log on paper, in a Log Book.
If you find a logging program you like, reply here (I'd like to know what others' find helpful).