This is a step-by-step of how I setup my MessagePad2100 from a BrainWiped state.
In the package lists, I've linked directly to the UNNA entry for the package where possible.
Since I'm a Windows user, I'm stuck doing my package installing via a WindowsConnection over serial. So the first thing I do is install 
Ser57600 and then hack my registry settings for NCU, so I can connect at 57600bps instead of the default 38400bps and install things a bit faster.
After that, there's some basic enhancements to the NewtonOS
and applications that I just can't live without:
- Big Notes - lets you create Notes over 4k in size
- EEUnProtect - ignores the copy-protect bit on all installed packages
- IO Box Select All - Adds a Select All button to In/Out
- Pkg Info - adds a routing option in Extras to get a package's information such as size, copyright, version etc.
- alt.rec... - enhances and improves the printed recognizer Rosetta
- SBM Options - tweak little settings like # of clipboards, battery warning level, etc.
- Heaven or Hell - avoid the nasty -10061 error
- DashBoard - it's like NewtonOS 3.0
- Dreamsoft Spell - spell checking in Notes
Next are drivers for all of the external doohickeys that extend my Newton:
- Ethernet card drivers or WaveLan drivers - requires Newton Devices to be installed first, at minimum
- ATA Support for CF cards
- PReader package for my Siemens Pocket Reader
- InPath for my barcode wand
Internet packages are always important!
- NIE 2.0, Internet Setup, and NIE Patch v2
- NIE Ethernet
- TCP/IP Dock package for making TCP/IP dock connections to DCL, EScale, or DILTester
- SimpleMail for full POP3/SMTP and basic IMAP support
- Web browsers: lately, I favour Courier
more to come...
