Using portable software is really great, if you have a use for it. For example, if you are in school and have to work on a school computer, it’s likely you can use your portable apps on that computer, and keep your profiles/files on the USB. Having your files and programs go with you, wherever you go is very convenient and useful.
There are no real cons to using portable software on a USB. Everything is stored on the USB, so you can easily move from computer to computer. Also, it doesn’t ruin the USB or anything. You can still use it to store files, and you can easily remove the portable applications if you find that you don’t need them.
The variety of software available for portable devices is actually quite astounding. There are games, Office software, email clients, media and graphic editors, browsers, and other security software such as anti-virus programs. You can make a portable tech support kit on a USB device if you are constantly having to help other people with tech problems.
As @mrentropy said, PortableApps.com is a great website and Portable Applications suite. I used it for a long time when I was forced to use a school computer. There are hundreds of software applications that have been made portable by the vast community, and you are bound to find something that you find useful. The suit comes in many types with default applications on some, so you can choose the one that will fit on your USB and customize it as you see fit.
Also, as @dverhey said, U3 sucks. I had it on one USB thumb drive I had, and it really sucked. The application selection is very limited, and it’s very bogged down with pointless stuff you will never need. I would recommend simply removing all of the U3 files and installing another suite. U3 is just not worth having on a USB jump drive.
If you are going to be on a mac, then you will have trouble using PortableApps. There are other applications that will work on a mac, however. I did a quick google search and found this blog post with 100 Portable Apps for Windows and Macs. You should give it a quick look through and see if you can find any applications that you think would be beneficial to have available on a USB drive.
Also mentioned in that blog post is an entire portable suite of applications similiar to PortableApps, for a mac. It’s called FSuite It comes with 30 applications for word editing, gaming, and browsing the web. It’s less customizable and community driven, unfortunately.
I don’t see a need for portable apps any more, sadly. I have purchased a Netbook (Samsung NC10) and use it for notes at school. So I can simply store all my programs on it and not worry about space. Also, I use Dropbox to sync my files from my Netbook to my Desktop at home so I can work on them at either locations and send the updated file back and forth. I can also download any file I have saved in Dropbox using their web interface. Because it’s free with a good amount of space (and paid upgrades for more space) it’s a great solution for my needs. You can even store the PortableApps suite inside of Dropbox, so it syncs your portable software applications settings between computers.