Some of the major ones that I use or that can be used to make it a very functional workstation.
AppleMenuOptions.app : This was developed after RDR2 was released and was included in Mac OS X Server 1.x. It lets you configure the Apple menu in almost any way you like (mine is very much like my Mac OS 9 Apple menu actually).
Calculator.app : Doesn't come with the OS, but you can find it at either Peanuts or Peak, and use ProjectBuilder to compile it. It is not that different from the Calculator of the Mac OS.
Create 5 and the Stone Design Suite : Andrew Stones collection of apps that do a ton of cool things (you can read more about them at stone.com).
Fiend.app : Apple dropped the dock after RDR1, so Fiend jumped in and gave it back, works very much like the old NeXT dock, specially if you set the Workspace Manager's preferences so that minimumizing windows sends them to icon at the botton of the desktop.
Mesa3.app : Nice speadsheet program (if you need a spreadsheet app)
OmniPDF.app : This is a
very beta version that was not stable for me (it would crash almost anytime I opened a pdf doc).
OmniWeb.app : Full version of OmniWeb 3 (thanks Omni for making one for Rhapsody for Intel) that works great.
PDFView.app : This is how I actually view all my pdf docs in Rhapsody, it can read anything that Acrobat Reader 3.0 can read.
TextEdit.app : This is the app that most Mac user dismiss as
just SimpleText for Mac OS X when it is actually a feature rich word processor (that allows you to add images and spell check).
MailViewer.app : Basicly the same as Mail.app from NeXT, and function like Mail in Mac OS X
TIFFant3.app : Image Editor, almost in the same league as Photoshop, but takes some time to get use to (see caffine software's web site for more about itls set of features).
WriteUp.app : This is as complete a word processor as any I've ever seen, same league as Word and WordPerfect.
PasteUp.app : About on par with PageMaker 5.0, but still a very feature rich page layout program.
Stickies.app : You guessed it.
TinyInstaller.app : Rhapsody does not come with an installer app (Apple dropped the NeXt version and wouldn't replace it until the release of Mac OS X Server 1.0), so you have to use the command line
installer.sh which can be a pain. This little app adds a GUI to that command.
Chess.app : Same as both the Mac OS X and NeXT versions (how could they improve on perfection).
QuickTimePlayer.app : Nice QuickTime 3 application, if you have the full version on some other system you can convert even the latest Star Wars trailers so you can watch them in Rhapsody.
RhapsoDoom.app : If you have the full version of Doom or Doom II, you can get them up and running in Rhapsody (this is a beta version, and not totally stable, but still playable).
Hextris.app : Tetris type app, fun to kill time with.
Risk.app : Beta version of the game Risk.
Solitaire.app : Scott Anguish's version of the greatest time killer of all time.
Balling.app : Another great time killing game.
I think that covers most of the stuff that I use that I consider of mildly important. They range from freeware to semi-expensive (TIFFany is about $500, WriteUp in in the $300 range, and Create was about $200 that last time I checked). All and all, these apps make Rhapsody a very livable computing environment.
I currently have a collection of some 300+ fonts, many of which can be found at
http://www.peak.org/next/fonts/ , installing them has something of a trick to it (you have to use the terminal.app if that gives you any idea what is involed)
Places to go:
http://www.peanuts.org/
http://www.peak.org/apple/rhapsody/
http://www.stepwise.com/