Since the 99% of programs are installed at Computer level, no you cannot.
You could bypass the issue installing the same programs on all computers the user will need to logon. Profile will carry the (user level) settings.
Another option is to virtualize the applications. Basically it consists in setup and configuration capture and "packaging" of all the new files and registry entries in a single and portable package. After that you can copy this package in the roaming profile and link the main exe where it suits the user best.
VMware ThinApp is the best solution to do so otherwise you'd can also evaluate Cameyo (free & open source) and several others: http://alternativeto.net/software/vmware-thinapp/