I made an update after I found that WinSCP can accept an INI and log location passed on the command line. Now the WinSCP launcher doesn't have to stick around.

I've just posted a test release of WinSCP Portable 4.0.3. It's WinSCP packaged in PortableApps.com Format so that it automatically integrates with the PortableApps.com Suite and works from any portable device (USB flash drive, iPod, portable hard drive, etc). It will automatically work with PuTTY Portable (just start PuTTY Portable before clicking the PuTTY button within WinSCP).

For more information and to download the test release visit: WinSCP Portable 4.0.3 Pre-Release 1 (Testers Needed).

Thanks,
John