I think the example you mention (Gap) is pretty typical. Here are a couple of others that follow the same pattern:
- West Elm (westelm.com) - links to Pottery Barn and other partner sites in the header. Copyright consistant in the footer across all sites. Each individual site branded and organized independantly (with some similarities)
- Google - links to the different services in banner at the top, each has very distinct layout and navigation
In the first examples (Gap and West Elm) the sites are likely kept separate for marketing reasons. A nearly identical product sells for 3x the price between Banana Republic (http://bananarepublic.gap.com/browse/product.do?cid=35922&vid=1&pid=813533&scid=813533002) and Old Navy (http://oldnavy.gap.com/browse/product.do?cid=5251&vid=1&pid=681353). The sites are being kept separate so that the brand differentiation can support the pricing and positioning tiers between different customer segments. It would be quite simple (from a IA perspective) to merge all of the actual products into one navigation structure - but if they were all in one site I would see the cheaper t-shirt and be more likely to buy it.
In the Google case, the different sites are kept separate because the user is completing very different tasks between GMail, Google Docs, search, Google+ etc. In this case it makes sense to separate the sites based on the users task, merging could be a very messy prospect!
Without knowing why your users may want to switch between sites, I think having category or brand links in the banner of the page is a fairly universal pattern and is likely to fit your needs.