No danger, the PortableApps.com people have done a very nice job here and elsewhere.
Most software isn't really written to be portable. The usual workaround is to copy the APPDATA info to and from the flashdrive, and run drive letter replacements on the configuration files.
(Some applications, like calibre, allow you to specify where the APPDATA should go via an environment variable. That helps avoid errors in cleaning up behind itself, and maybe race conditions when exiting in an abnormal fashion.)
But you probably don't care about how PortableApps are portableized
just be happy it works.
Any apps on the official distribution list are guaranteed to work. They just aren't guaranteed by the application developer -- rather by the PortableApps crew. (Again, with the exception of LibreOffice.)
Open-source applications FTW.
