I use Sandisk Cruizer 4GB U3.
U3 Partition:
1: emulate cdrom
2: pendrive
I write script and build iso file which scans disks in the background,search is the file "\PortableApps\PortableApps.com\PortableAppsPlatform.exe" and runs it.
Work 100%
In my site are all file to download.
http://free-portal.pl/download.php?view.7
Instruction:
1. Download pack: "U3PortableApps.rar"
2. Unpack in C: (Easy to use file in dos)
3. Run u3.exe in dos
4. write and enter: u3 -p 1024000 x {x-letter to pendrive, repartition device 1mb}
5. write and enter: u3 -l U3PortableApps.com.iso x {x-letter to pendrive, load iso image into device}
6. Run normal install PortableApps in partition 2:pendrive
7. end and fun 
If you have any problem post comment in my site
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will this wipe my flash drive if I use it?
If you have pendrive U3 - Yes others NO
You can try use u3.exe and write u3 -i x (x letter pendrive)and enter
If you see:
Total device size: 3.77 GB (4047503360 bytes)
CD size: 1024.00 kB (1048576 bytes)
Data partition size: 3.77 GB (4046454784 bytes)
- My mod 100% WORK ! ! ! in your pendrive.
If you see:
u3_partition_info() failed: Failed executing scsi command: Error 1117
- My mod NOT WORK ! ! !
/////////////////////
I working apps for all device
Please If you found bug send to me all information
KevMyst
are you saying your mod can partition ALL devices, not only U3?
Partition Only u3, but i working new version.
KevMyst
Similar to what you've just done, I've been gathering necessary tools, sources, and examples together in one place. I haven't looked at your workflow, but it is consistent with a direction I took.
My goal was to create a Makefile that automated the creation of EXE autorun program, the building of the ISO, and flashing of the U3-CDROM - all the pieces necessary to build and rebuild a U3 autorun program.
See:
https://github.com/jleonard99/U3-autorun#readme
Other related links:
https://portableapps.com/node/3338
https://portableapps.com/node/27625
http://sourceforge.net/projects/u3-autorun/
http://www.uwe-sieber.de/usbdlm_e.html
http://en.wikipedia.org/wiki/AutoRun
http://en.wikipedia.org/wiki/AutoPlay
Good search keywords on Portable apps site:
U3 autorun
Disclaimer:
This post is not advertising for a new portable app. This post is a breadcrumb collecting tools and examples to offer someone interested in developing new U3 autorun tools a starting point. I spent way too much time surfing to find all this stuff, and hopefully this post will save others time!