I used to own an SL-5500, then sold it, then bought an SL-C1000 a few months later.
I originally sold my SL-5500 because I couldn't deal with it anymore. Due to a sizeable bit of stupidity during the first few days I had my 5500, I plugged it into a 6V power supply, which blew the internal battery charging mechanism. The rest of the unit was fine, but I had to buy an external charger for my battery.
However, there were other things that I disliked about the SL-5500:
It did not have a fast enough processor to decode well-encoded DivX movies (one of my main intended uses) or to run emulators well (another of my main intended uses). The contrast of the screen was poor, and when trying to show different shades of black it would get all messed up. The screen resolution was not too great, especially when trying to view webpages. The keyboard was a bit too small for me to comfortably thumb-type on. The internal flash was not large enough to hold all the programs I wanted to install - I had to reformat an SD card and use it for applications. One of the hinge connectors on the plastic screen cover broke, and I had to super-glue it back on, but the cover was still loose so my screen got dirty.
Most of all, the battery life on my unit in particular was abysmal. I bought it used from a friend for a really low price, so it may have been that my battery was nearing the end of its lifespan, but I was rarely able to get over 1 hour of use out of my unit.
So on to my SL-C1000 - it is everything I wanted the SL-5500 to be. The processor is fast enough to run emulators and play movies, the screen contrast is noticeably better (more on that in a second), the resolution is impressive and is just right for web pages, the keyboard is bigger, the internal flash is large enough to hold all my applications, everything on the unit seems very sturdily constructed (I did worry before buying the unit that the flip-around screen would perhaps become weak over time, but the hold flip-out and around mechanism feels so solid that I'm not worried about that anymore), and the clamshell design keeps my screen from getting too dirty.
And, most of all, I am astounded by the battery life. In order to test the life, I devised what I like to call the Lord of the Rings video stress test. I ripped LotR - Return of the King, compressed it to a 700MB DivX file and copied it to my 1GB SD card. I then charged my SL-C1000, put it on full brightness, connected my Shure E2C earphones, turned the volume up to a reasonable level, and opened the movie in mplayer with a Kino2 frontend, bvdd drivers installed. I was expecting my Zaurus to run out of batteries 2.5 to 3 hours into the 3:20 movie. That did not happen. Instead, it made it all the way through the movie, then through two 20 minute episodes of Futurama, then about 10 minutes into some light text editor use, before it finally turned off. The total run time, with the screen brightness on full and the sound in my headphones on, playing DivX from my SD card, was 4 hours and 15 minutes.
The only thing that dissapoints me about my SL-C1000 is that the screen is so very hard to read in direct sunlight. Note that it is still quite useable on a bright summer day outside in the shade, but if I'm trying to make a note or something while walking around outside, it's a bit difficult. Many people also complain about the lack of internal wifi, but Wifi CF cards are a cheap and effective solution to that problem. I suppose I should note that my SL-5500 was no better at showing the screen in direct sunlight, but I believe I have read that SL-6000s use a different screen lighting technology that looks much better in intense external light.
Apart from everything I didn't like about my SL-5500 being improved, I enjoy the SL-C1000's new features, too. It looks nicer than the SL-5500, the flip-around screen, though I don't use it much, is still useful on many occasions, the keyboard is not only bigger but has more keys, which makes entering non-alphabetical characters easier, and, of course, the USb host is quite awesome. You can hook up any keyboard easily and it will instantly be recognized. External USB can usually be used with little hassle, as long as you set thing up first, and I am exploring more exotic peripherals such as external USB drives and webcams.
My favorite peripheral is my iRiver ihp-120 20GB mp3 player. I was able, after mounting it via the command line, to connect my music player as an external hard drive and use it to store more than one full-length movie while on the go.
In short, the SL-C1000 is a wonderful machine, and with the USB host port available on all of the four-digit SL-C models, the 4GB internal hard drive is not really that important. As long as you can manage to spare enough money for the SL-C1000, definitely go for it. If you can't get enough money together, I would recommend at least buying an SL-5600, with a faster processor and almost twice as large battery.
All that being said, I don't think the SL-5500 is a bad machine, and if I had bought one new and had been less clumsy and stupid with it, I might still be using one.
Also, if you do decide to get an SL-C1000, I would highly recommend StreamLineCPUs/TriSoft, who do a great job with english conversion, offer incredible support, and, though they are not as cheap as pricejapan.com or conics.net, are still significantly less expensive than Dynamism.
(Hope that wasn't too long)
P.S. - The SL-C3100 won't be out until June 24th, so it wouldn't be available at places like Dynamism right now.
