I've used GNU/Linux since (February?) 1999. I started with Slackware, and now I'm running Ubuntu. I think Linux is fantastic, but one thing always irritates me.
Whereas MS-Windows has a 'Program Files' directory with a sub-directory for each application, Ubuntu stores application files across the file-system according to type, eg. /etc, /var/log, /bin. I find the Windows approach much easier to work with. The Ubuntu method means it takes much longer to find where things are. For log files it may be easy, but where is the webapps directory for apache-tomcat?