These devices are getting to be affordable, small, and high capacity:
http://www.wdc.com/en/products/Products.asp?DriveID=199
I own one of these and I love it. It really is as small as it looks, and it keeps well in a small pouch in my backpack. I bought it from the WD Store but I'm sure you could find it 40% off at some discount store online (although if it breaks, good luck getting any help from them.)
For comparison, it's about two thumb drives thick and one and a half thumb drives long. Depends on the size of your thumb drive of course. I haven't (intentionally or accidentally) given it a physical beating to test its ruggedness, since it is an actual hard drive and not a stick of flash RAM... but when you consider that you would need about 60 expensive USB sticks at 2GB each to match this $199 120GB hard disk, you need this (or one of the cheaper models, even) if you use as much space as I do. I just got it a month ago and I've already used 10 gigs on it! Anyone have a 10 gig flash drive? hehehe 
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All depends on what your needs are. I keep my flash drive in my pocket with my cell phone when going to business meetings and such just in case. I also throw it in my backpack when traveling just in case and don't worry about the bag being banged around. Flash drives will survive a lot of things that portable hard drives just won't (including being accidentally sent through the washing machine or dropped in a puddle).
Sometimes, the impossible can become possible, if you're awesome!
I've got one of these on my Amazon wishlist. I currently use a USB memory card adapter and a couple of 1GB SD cards. I only use up about 250MB max on each card... leaving plenty of space to copy big files (movies) between machines when needed.
I'd prefer something rugged - just like John mentions. I throw my bag all over the place and happily keep using my USB sticks.
First tried using an older 4GB portable drive and now my 20GB iPod.. both are giving me troubles with my laptops... after a while the computers start freezing and locking up... and then later perform disk checks for consistancy. The best I can figure is it might have to do with read / write speeds, but I'm not sure... but I DO know it's not a virus or spyware... something is not going well for my external drives being used for portable apps...
Jds
The computer freezing or locking up while using a USB-based drive -- whether flash or hard drive-based -- usually indicates either a hardware issue with the device itself... or a hardware or software issue with the computer. Since 2 different drives gave you problems, I'd wager the issue is with your laptop. If all software is as expected, it could be a bad device driver or a hardware issue.
The only time I've run into this problem was with a bad device. My old external hard drive's controller was going. A new external case with a new controller solved the problem nicely.
Portable apps even work over USB 1.1... just very slowly. At no point would they freeze a computer that didn't already have issues.
Sometimes, the impossible can become possible, if you're awesome!
I was afraid of that... I have had troubles with 2 laptops and 2 HDs, but one HD is much older and it was giving me trouble with laptop #1... so perhaps it was the HD on that one... but the iPod gives me trouble on laptop #2 quite often, but almost never (well, never) on Laptop #1...
Laptop #2 has a HD which I believe might be dying... or at least I have been suspecting such... I was hesitant to claim this problem as the laptop's as I had similar problems on two machines, though from what you say, it really much be 2 separate problems related to 2 separately faulty HDs... *sigh* Time to break out the wallet and get a new HD...
Jds
At college, on the lab computers (which have like, no software, but they allow you to plug in USB drives), the USB interface version is 1.1, but my portable hard drive needs USB 2.0 for full speed operation. On top of that, their McAfee virus scanner scans everything that is read from the drive -- their On-Access Scan is set to scan everything, without the ability for me to change that.
McAfee also sets its process priority very high, by default -- so, if I launch a 50 megabyte executable, I have to wait about 20 seconds while the executable gets transferred to RAM for McAfee to scan, then an additional 5 seconds for McAfee to scan it (and it takes up 100% CPU during this time), and then it allows the executable to run.
You may be having the same issue. USB 1.1 will cripple any device designed for USB 2.0. You just won't get the performance you want. I know it's not the drive, because on my speedy home computer (with McAfee disabled most of the time, and USB 2.0 ports), it never lags the system when I transfer or launch huge files on it.
Actually, John called it... just a few days later, I got solid confirmation that it's the HD going bad as an unbelieveable SCREEEEEECH noisy came from the HD, twice! Somehow, the monster still booted, though slowly software became corrupted, disk errors are popping up like mad, sound no longer works..
So I ordered a new HD from Newegg. And in the meantime, I reinstalled the OS to make up for the HD errors (for now.)
*sigh* Pain in the rear! And my iPod is broken too... *sniff, sniff*
Jds
panasonic just release 4GB SD card ... I think it's even better sicne it is flash drive not normal drive ..
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