There are plenty of books on Mac OS X, but look for one that is aimed at Windows converts as most are aimed at Mac OS 9 updraders.

These articles introducing the Unix command line might help:
http://db.tidbits.com/getbits.acgi?tbart=07003
and
http://db.tidbits.com/getbits.acgi?tbart=07068

I'd recommend installing a new web browser to replace the sluggish IE (although IE is useful for sites that insist that they need IE to run because the coders were lazy). Safari is the favourite for most users, but Camino is generally better and uses the Mozilla rendering engine so tends to be more compatible.

If you've looking for software, VersionTracker is a good resource that lists almost every software release for the Mac.

MacNN is the stalwart news site and is useful for getting up-to-speed with all things Macintosh.

You may notice that the new PowerBooks have a 'feature' where sound goes to sleep and takes a couple of seconds to wake up (making a noise in the process). This fixes it.

Proteus is a good instant messaging client that supports ICQ, AIM, MSN and Yahoo. It has a few more useful features than iChat too.