Image by valentin.d via FlickrI've been working with portable applications for too many years to count. Since I started I've written a help file which tries to explain the basics and gives brief reviews of a few launchers. At one point I started using LupoPensuite which was based on the ASuite launcher. As I noted in the my help file, ASuite has some problems, which is why I stopped using it. Anything based on Asuite, including the recent runner up in Lifehacker's Poll of best portable suites, LiberKey, seems to put all of the applications in an apps folder with subsequent applications in a separate folder. This is fine if you never look at the underlying structure of the directories, but if you care at all, it's a mess. Having hundreds of folders, each a seaparate application, to deal with when they are not categorized is a recipe for disaster.
The best part about LiberKey, in my opinion, is that it updates the suite and the applications automatically. This is an excellent feature and should be part of every launcher suite.
Lifehackers first place portable application suite, Portableapps.com, is an excellent platform, but it has the same problem as the ASuite launcher; all the applications must be in a subfolders of the portableapps folder. Again there is no categorization and worse there is no way to categorize the menu system itself (ASuite breaks down everything into categories in the menu system, even if they are a hodgepodge in reality). There is no doubt that the portableapps.com format is excellent (.paf.exe), but the fact that it will display all .exe files (although a recent change allows you to hide some applications you don't wish to display, this is a slightly backwards way of doing things in my opinion) in the main directory of each program makes adding portable applications that are not in a portable wrapper from their website confusing. Many times executables, like config apps will show up even if you don't want them to.
I found that the PStart menu system, although not bundled with a slew of software, is highly preferable. It allows you to specify your own directory structure on the portable device you are using. You can also decide which files you want to show up in the menu system. It certainly doesn't have the glitz or glamour that portableapps does, but it is much easier to configure and use, especially when you have more than 15 or so apps. I have 8 gigabytes worth of applications from all over the web on my stick. Pstart keeps everything categorized both in the menu and on my stick in the correct directories. All the portable programs I find work with this menu. (the only trouble I've run into so far has been portableapps .paf files of Google Chrome and Skype, both of these had to be installed in an upper level directory because the path was too long where I wanted to install them - u:\utility cd\usbportable\internet\browsers\googlechrome and u:\utility cd\usbportable\internet\misc\skype. They ended up in u:\
Bottom line is that if I could have voted for PStart in the lifehacker poll, I would have, unfortunately PStart is not a suite, just a launcher.