Apps in Non-Standard Directories

What programs are they? They may already be portable-ized.

Q. Do these apps already run from the drive as-is, if you browse to their exe and run them?
I'm not going to ask if they fit the strict definition of portable, you'll have to work that out if it's an issue.

A. If they just run OK, then you can put them into the menu by setting up dummy folders with the right paths in the appinfo.ini files. The Start line in the appinfo.ini uses a relative path to start the app, and you can fool it into pointing almost anywhere (relatively speaking)

Assuming that your PortableApps is installed in the root (X:\) and that your cool tool is in X:\BootCD\cooltool.exe...

Make the following folders/file:
X:\PortableApps\Cooltool\App\appinfo\appinfo.ini

Contents of the appinfo.ini:

[Format]
Type=PortableApps.comFormat
Version=2.0

[Details]
Name=CoolTool
AppID=CoolTool
Publisher=DevName
Homepage=CoolToolHomePage
Category=Other
Description=CoolTool Description
Language=Multilingual
InstallType=English

[License]
Shareable=?
OpenSource=?
Freeware=?
CommercialUse=?

[Version]
PackageVersion=x.x.x.x
DisplayVersion=x.x.x

[Control]
Icons=1
Start=..\..\..\BootCD\cooltool.exe

The lines you need to keep the same are in the [Format] section, and the Name= will be the displayed name in the menu.

Why does this work? The Start= starts from the expected location of the app launcher. We set a relative path by using "..\" to move up a level, and then follow the path to your exe. If your tool is in a different location, you will have to adjust this path in the appinfo.ini.
Important: If you find you need to tweak the path, make sure you save the appinfo.ini and Refresh App Icons every time, or your changes will not be applied.

A.2. You could also use RocketDock or Cylog Toolbox (my fav) that would run concurrently with the PortableApps menu - you could even Autostart these so they always come up. It's MUCH easier to add relative-path shortcuts to these!