IMHO, then the nicest and cleanest method of installing apps without an installer, is by using an INF file, like e.g. this one for Foxit Reader:
CODE
[Version]
Signature=$Windows NT$
[DefaultInstall]
CopyFiles=copyfiles
AddReg=addreg
UpdateInis=updateinis
RunPostSetupCommands=runpostsetupcommands:1
[DestinationDirs]
copyfiles=16422,Foxit Reader
[copyfiles]
Foxit Reader.exe
Foxit_JS_ExObjects.dll
fxdecod1.dll
js.dll
[addreg]
HKCU,"Software\Foxit Software\Foxit Reader\MainFrame","ShowEditorAd_908",0x0,"0"
HKCU,"Software\Foxit Software\Foxit Reader\MainFrame","ShowReaderAd_908",0x0,"0"
HKCU,"Software\Foxit Software\Foxit Reader\MainFrame","ShowTypewriterAd_908",0x0,"0"
HKCU,"Software\Foxit Software\Foxit Reader\MainFrame","ShowPOAd_908",0x0,"0"
HKCU,"Software\Foxit Software\Foxit Reader\MainFrame","ShowSDKAd_908",0x0,"0"
[updateinis]
setup.ini,progman.groups,,group1=%16409%
setup.ini,group1,,"Foxit Reader,""""""%16422%\Foxit Reader\Foxit Reader.exe""""""
setup.ini,progman.groups,,group2=%16410%\Microsoft\Internet Explorer\Quick Launch
setup.ini,group2,,"Foxit Reader,""""""%16422%\Foxit Reader\Foxit Reader.exe""""""
[runpostsetupcommands]
%16422%\Foxit Reader\Foxit Reader.exe -Register
This INF will make a folder in %programfiles% named 'Foxit Reader', copy the four program files over to that folder, make shortcuts on the desktop and in quick launch, add reg-entries for diabling adds, and registering file-associations.
All the 4 program files + the above INF should be in the same folder, but if wanting the 4 program files into a seperate folder for "cleanlines"(so it's an INF + a folder with the source files), then just change the 'copyfiles' section like this:
CODE
[copyfiles]
Foxit Reader.exe,files\Foxit Reader.exe
Foxit_JS_ExObjects.dll,files\Foxit_JS_ExObjects.dll
fxdecod1.dll,files\fxdecod1.dll
js.dll,files\js.dll
(No need for SourceDisksNames/SourceDisksFiles

)
Note: The above is an Advanced INF and hence needs to be installed through advpack.dll:
CODE
rundll32 advpack.dll,LaunchINFSection install.inf,,1