I have been on the lookout lately for some good tools to fill up my flash drive  and I thought I would ask the Server Fault community for recommendations on good tools that will fit onto a thumb drive.
These are the utilities I have on my drive:
Beyond Compare , brilliant for checking for changes http://www.scootersoftware.com/
Most Previously SysInternals Tools 
In top of that, I strongly recommend to add TrueCrypt  if you keep any personal or confidential data. Sometimes I need to put customer's database backups and I'd be in great trouble if someone gets access to them. http://www.truecrypt.org/
I got these from crazeegeekchick.com  some time ago and I really love them.
TrueCrypt  – encrypt your thumb drive to protect your information
ToDoList  – A task management tool that allows you to repeatedly sub-divide your tasks into more manageable pieces whilst still presenting a clean and intuitive user experience. (Windows Only)
Portable Firefox  – Leaves no personal information behind on the machine - you can take along your browser/extensions/bookmarks anywhere
Pidgin Portable  – All-in-one instant messaging (supports AIM, ICQ, MSN Messenger, Yahoo, G-Chat, etc)
WS FTP32  – ftp client
FileZilla  – yet another ftp client
Notepad2  – a fast light-weight advanced text editor with syntax highlighting
Notepad++  - this is one of my favorite text editors – now made portable
Color Cop  – this is one of my favorite freeware apps – includes an eyedropper you can drag over any window to grab the color value. It then offers a palette of 42 complimentary colors to the one you've picked.
Ifranview  – a light little graphics viewer/editor that packs a big punch. You can use it to work with screen captures, create slideshows and more
GIMP  – the popular open source image editor packaged as a portable app – very robust
7-Zip Portable  – handles zip, gzip, tar, rar etc
Allway Sync  – syncs files between your thumb drive and PC
Unknown Devices  – helps you find out what the unknown devices in the device manager are
TestDisk  – data recovery software that can recover lost partitions or make drives bootable again
UTorrent  – my preferred bit torrent client – I love having this with me wherever I go
Roeder's .NET Reflector  – recently purchased by Red Gate, this still-free app can be used to explore .NET assemblies, understand relationships between classes and methods, find where types are instantiated and exposed or check that code has been correctly obfuscated before release. There are also over 30 add-ins available.
Process Explorer  – formerly Filemon and Regmon, this is an invaluable sleuthing tool
TightVNC  – based on the popular VNC remote control software, this version can live on a thumb drive
WinMerge  – compares differences between files and merges changes. It has the same features as the desktop version
Text2Html  – a text to HTML converter – converts text files into HTML format
Portable Apps Suite  – this is the mac-daddy of them all – it includes Firefox, Thunderbird(email), Sunbird(calendar),ClamWin (antivirus), Pidgin(see above), Sumatra PDF Readable, KeePass Password Safe, OpenOffice, CoolPlayer (audio Player) and even a couple of games
Restoration  – Recover accidentally deleted files – even after they were deleted from the recycle bin
Infra Recorder Portable  – cd and dvd burning
RockXP  – allows you to recover windows passwords or keys, change keys, display system password, and more – sneaky!
[Update: Initially I deleted this answer because I spotted it was already mentioned in the question. However I think it would be good for it to see votes so I have checked the Community Wiki box to prevent people from thinking I'm trying to game the system]
Apps from http://portableapps.com/ like Portable Firefox leave no trace on the system you run them on.
Also the PortableApps app itself makes using them a piece of cake.
What doesn't fit on a thumb drive, these days? 16GB drives are like $50!
Linux  (e.g. Debian , Knoppix , Puppy ). Even if the systems you're working with aren't Linux, you can get useful things done by having a full, working OS in your pocket; sometimes having a different OS can even be an advantage. http://en.wikipedia.org/wiki/Live_USB
Wireshark - monitor network traffic.
In addition the Sysinternals, AVG, Portable Firefox and PuTTY mentioned above my USB key contains:
One of my most-used tools on my USB-Stick:
It's about the easiest and quickest (regex) find/replace tool available.
A decent text editor (eg. notepad++). Process Explorer.
I usually keep about a dozen different types of boot-images on my USB (and yes, it doesn't cost an arm and a leg to buy all this stuff):
The main reason being that when you work with governmental organizations, you can't always get access to the Internet, but (for me) it was easy to burn CDs there. It made debugging bad hardware, and problemtic OSs much easier. http://grc.com
Definitely Total Commander . Just runs out of the install folder; does packing/unpacking, FTP, file diff, folder sync, multi-rename, checksum generation/verification. You name it...
For those who still own POP3 accounts; E-Res-Q  (shameless plug!) allows no-frills access to a POP3 account for quick viewing and cleanup of messages (good for clearing spammed out or blocked-with-a-50MB-attachment accounts). http://ghisler.com
DosBox  of course, for when you need to emulate an old ODS machine for, umm, old office applications. http://www.portablefreeware.com/?id=687
Aside from SysInternals, utilities from Nirsoft  are also useful. http://www.nirsoft.net/
Installers for perl and vim
Portable Total Commander is a must have for any portable environment.
Win32 GNU tool set
AutoHotKey  can be placed on and run from your flashkey.
There are many things you might script an ability to do which might ease Server related tasks. http://www.autohotkey.com
I really like http://portableapps.com/ for this.
This question is 7 hours old, and no one have mentioned a hex (binary) editor yet. Sometimes, even a sysadmin needs to look inside a file to check (or tweak) what realy lurks inside.
Lightweight but a little old, frhed  a is free binary file editor for Windows.
HxD  is a carefully designed and fast hex editor, seems more current. http://www.kibria.de/frhed.html
Make a thumb drive that is bootable to Ubuntu.
For constantly updated info on this, check out
Directory Opus , it feels like half of your computer is always with you. http://www.gpsoft.com.au
Maybe take a look on Framakey  which is a compilation of modified program to use them on a USB stick.
It currently includes :
The Computer Repair Utility Kit that Technibble put together has most of the essential tools you'd need. It's been designed so that the tools can run from a USB drive. Unfortunately, they no longer distribute the toolkit themselves, but you can probably find a copy elsewhere.
Technibble also has lots of reviews of sysadmin tools.
I'd say having a bootable WinPE image is crucial for desktop/server support.
Far manager , of course, besides the stuff other mentioned. It is like Total Commander, but what is interesting about it is that it is a Windows console application - but it displays full UI. http://www.farmanager.com/
To mention a few I don't yet see listed:
I work with a lot of MS-SQL installs so I always have a copy of the old (no longer shipped) odbcping.exe. Last Microsoft SQL version to ship it was SQL Server 2000 (afaicr).
Very useful to determine if there's a problem with a SQL Instance.
usage: odbcping [-S Server | -D DSN] [-U Login Id] [-P Password]
moveable python  http://www.voidspace.org.uk/python/movpy/
You can get UBCD4WIN on a thumbdrive
Installer for AVG anti-virus.
VPC 2007 and Two VHD's:
I just loaded up my thumb drive with:
I have another thumb drive that is a bootable live Linux which comes in handy for gparted, dd, etc.
sysinternals was already mentioned, but I wanted to point out Desktops  explicitly. It's an awesome tool when it works.
Desktops allows you to organize your applications on up to four virtual desktops. Read email on one, browse the web on the second, and do work in your productivity software on the third, without the clutter of the windows you’re not using. After you configure hotkeys for switching desktops, you can create and switch desktops either by clicking on the tray icon to open a desktop preview and switching window, or by using the hotkeys.
I know linux has been mentioned, but DamnSmallLinux  has a VM version > 50 Meg's it's pretty awesome. http://www.damnsmalllinux.org/
For disk usage, I've seen utilities that use treemap visualization mentioned, but not the ancient, small, and unfortunately named Scanner  (distributed as scn2.zip).
I find Scanner's sunburst chart much easier to read than treemaps, even if it lacks some of the features and speed of things like WinDirStat and SequoiaView. http://www.steffengerlach.de/freeware/
Use TiddlyWiki as a notebook: http://www.tiddlywiki.com/.
Ideal for carrying all your system-administration notes around on a stick. A full-featured wiki with wiki markup, links and tags in a single self-modifying html file.
OpenOffice! It's not perfect, but darned handy. There's a portable version too.
This way if I get to a machine that has some budget version of Microsoft Office, or heaven forbid MS Works, installed I have tools that I am used to readily at hand.
Spacemonger v1.4  for tracking down large files/directories. Free, small and colourful. http://www.sixty-five.cc/download/
Right now I have a 16GB OCZ Rally2 which I find dead handy. I keep lots of the tools mentioned above on it (in portable app form, mostly).
I've got the contents of some useful OSs on there: notably Windows XP, Server 2003, and also the Win 7 Beta. I created a partition that is compatible with W7 too so I can install directly without an optical disc. Dead handy for testing on laptops with varied hardware configurations.
Tor -- you never know when you're going to need Web access that is free from cookies, Java, and other plug-ins.
JkDefrag v3.36  - Better than the Native Windows disk degfragmenter. It can run from your USB drive. And best of all, it's FREE! http://www.kessels.com/Jkdefrag/
Look at the PC Repair/Toolkit 
If you need to view/edit XML files of any type I highly recommend First Object XML Editor .
Lightweight, no install, tree-view/editor synchronisation, syntax highlighting, and best of all a customizable Indent option (F8) to make sense of crazy Microsoft config files ;) http://www.firstobject.com/dn_editor.htm
Drive Snapshot disk imaging tool:
No installation necessary, so you can just run the EXE on any host (Windows) to create a disk image to an external drive or network location.
I have a bootable Ubuntu USB thumb drive(recently updated to 9.04), It has saved Data from many dead laptops and PCs.
I like this USB software package -- http://portableapps.com/
Just wondering... How big is that flash disk supposed to be? I myself have one that is 32 GB and there's a lot that you can fit on that. ;-) If you use it on a system that can boot from USB, you might even consider installing a complete operating system on it, to run from USB. (Most likely going to be Linux.)
I'm a fan of SIW (System Information for Windows). Lets you check a lot of computer information from a small exe file that fits on a thumb drive. It's got a free version as well which has always done everything I needed it to.
I would add the following:
Clonezilla Live, Knoppix and Trinity Rescue Kit are great for larger usb drives. I edit the syslinux.cfg file so all 3 are bootable.
Pendrivelinux : make your thumb drive bootable!
They also have persistent installs now: your-whole-pc-on-a-stick ;-) http://www.pendrivelinux.com/
I like to mention two old-school apps I use:
Windows NT 3.5 File Manager (winfile.exe). A single file that gives me raw access to the file system. For 2000/XP use the version that came with NT4 Service 4. Under Vista/7 the original version doesn't run anymore, but there is a patched version at http://people.ee.ethz.ch/~davidsch/vistafm/
4NT, a powerful command line interpreter, for the cases when Powershell is not installed. Sadly, the vendor discontinued it.
iperf and wireshark are good. Not sure why you'd use the other sniffer when Wireshark is around.
Win7 install/PE and ghost32 for PE.
I would probably find windows boxes unusable with FAR manager, or any OFM.