Well it looks like i finally reached a solution. I went through the following steps:
1. Fake phone user-agent string as a Sony Ericsson W910i using NetFront (it was the first 240x320 screen phone i found in 3's compatible list).
2. Download the Java version of Skype from 3's services page. You have to save it, not just run it, because it uses a root certificate the phone doesn't have.
3. Modify the jad file in a text editor to remove the root certificate lines.
4. Also modify the midlet-jar-url value to "address/filename" as opposed to just "filename". Without this the jad file will not find the jar it needs since the midlet-jar-url value in the file is relative and not absolute. The address is the same as the one from which the jad was downloaded, so the simplest way to do this is copy the location of the "Download Skype" shortcut on the 3 page, then replace the jad filename with the jar filename.
And that's it - run the jad and it installs and runs fine. Unfortunately there's no touch screen support, and the GUI is very slightly too big for the screen, but it's still completely useable. In the future I could probably repeat the process with versions for other phones to see what works best.
Also, I had to make a call to it before it connected properly and showed all the correct contact statuses.
It worked beautifully after that though - it uses iSkoot to make the call through 3's dedicated number just as i wanted it to. This means the free Skype minutes I have are used, and the call is routed through the front speaker and not the loudspeaker. If someone rings me with Skype it works just as well.
As an added bonus, I noticed i can let the it run in the background and put the phone in standby mode, and if someone makes a Skype call to me, the phone still rings just like with normal calls. This definitely makes the service much more useable, as I don't have to turn off standby mode to make it work all the time.
Incidentally, while I was at it I also got 3's new version of Windows Live Messenger (old one didn't work for me) and with the root certificate jad modification, that's working too. I didn't need step 4 for WLM though because the url path was absolute.
I've attached the modified jad files for anyone who might need them.
It has been brought to my attention that this version of Skype will not work in the Intent Midlet Manager that HTC provide with the Tytn II, because the softkeys don't function properly. It does however work with Esmertec JBed. Windows Live Messenger will work with both managers.
I also noticed that the jar files I uploaded quickly stopped working because the url path changed. I've swapped them with new rar files containing both the jad and jar files (make sure they're in the same directory when you run the jad).
As an alternative to step 4 above you can do what I have now done with these files and simply use the jad url's and the filename contained in the jad to find the jar file in your web browser and download it directly. Then as long as it's in the same directory as the jad and you have followed step 3, and made sure the jar url property is in this case relative and not absolute, you can install the files without needing to connect to 3.
Lastly, if you want to run the programs from your start menu instead of loading JBed first, and/or you want to get rid of the annoying popups you get because these apps are untrusted, look here: