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Anything is possible, it’s just how complex is undetermined. If you already have the other applications and if you have a team of developers, have them take a look themselves and give you an observation if they think it would be achieveable.
The folks at php|architect may be a good resource for development questions for Magento.
What kind of “embedding” are you hoping to do? The term is hopelessly broad, and you won’t get very good answers without laying out specific scenarios.
-do you want to couple Magento with a CMS site?
-do you want to show a full Magento in an iframe in another site?
-do you want to leverage RSS or a web service to pull items from Magento into another ste?
-would you like to embed the cart functionality into another application?