I'm a loooong time linux user. Started with slackware, then SuSE, then debian, then back to SuSE... then ubuntu finally got me off my SuSE love...
Learn apt and learn the command line. You 'kids' these days are too tied to the gui. X has a way of falling on its face if you aren't careful, so make sure you can do things on the command line in a pinch.
My fav non-standard app? tilda. The name comes from how you opened up the 'cheat' console in doom and quake. It's the same in ubuntu, except it brings down a transparent console window. I can't live without it.
Other than that, gnome-do is great if you are a gnome user. Ctrl-space and start typing in the app, then hit enter... no need to deal with the 'start' menu.
As far as gnome/kde: it is a matter of preference, but I was a loooong time KDE fan (SuSE is KDE), but when gnome finally matured and KDE went off on it's 'workspace' kick, I found that when I wanted to tweak the UI, it was simple in gnome and just... worked.... KDE gave me all kinds of options, but even when I fine tuned it, it still wouldn't work for me. I had a hell of a time with dual monitors in KDE (on a laptop... turn off the laptop monitor, and use 2 external monitors... still can't figure it out on KDE).
I, personally, hate wine. It's bloated, doesn't work half the time.... I would rather have virtual box (the full app, not the stuff you get from the canonical sources) with a WinXP or 7 install. You can even setup virtualbox to boot up your other partition if you walk through the instructions to do that...
Flash (adobe) has always been a PITA... causing firefox to slow to a crawl. But it looks like they finally fixed it a few months ago, so make sure you have the latest version.... and use chrome... it is soooo much faster on ubuntu than firefox.
Pidgin is the IM choice for me. It isn't the default, but the default (which is empathy, I believe) isn't as mature as pidgin.
I also suggest using the sun java jdk's over the open ones. The open ones have had memory leaks and crashes for me for applications, and has some weird compiler rules when I work on some complex java code. It also doesn't play well with eclipse.
I'm sure I'll think of more, but that's all I got for now...