I know exactly what you're talking about. A lot of programs out there seem to think they are the only programs you'd possibily want to use. I can't imagine what makes software developers think this will make you use the software more...
I still remember back when I used AOL Instant Messenger. Whenever I tried to start Outlook Express, it would immediatly shut OE down and start itself up instead. Quicktime kept respawning copies of itself in my system tray, and Microsoft Word insisted on being my program of choice for editing web pages.
Unfortunatly, I don't know of any solution other than to stop using such programs and switch to alternatives. GAIM, for example, is a perfect alternative to AIM, and OpenOffice is an excellent alternative to Microsoft Office. I believe there is an alternative to quicktime out there, but I don't know the name. If something about a program bothers you, it makes sense to stop using it and try a different one.