Link deep into the site at many different internal hubs from high PR pages.  That forces spiders into the depths of the site and forces them to chew their way out through unindexed pages.  These links must remain in place permanently if you want the site to stay in the index, because if Google goes too long without spidering a page it will forget about it.

A mistake that people often make is to try to place five million pages on a PR3 website.  That will not work.  Not enough spiders coming in.  For a site like you are talking about you might need many dozen healthy PR6 links or hundreds of PR5 links and quite a bit of prayer.   For a site as deep as yours you might need to link to hubs at multiple depths because Google does budget the amount of crawl that they will perform.  The spiders will die down there.

will Google recognize that i'm only promoting our own websites and see this as a bad thing?

Google is really smart and knows that people have been manufacturing links this way for a long time.

In my opinion, a better idea would be to merge all of these little websites into one big kickass site.

You can do more damage to the competitor with one battleship than you can with ten potato guns.

Also... one big kickass site with tons of information and resources usually impresses the visitor more than a hotdog stand with a lot of links to similar websites.

An effective way for a small business to succeed in search is to build an ecommerce site with an extensive content library or build a large information site with a store.  This should be done without concern for which type of page gets the top ranking, and with a plan to direct content-consuming visitors to sales pages.  Most businesses do not take this route because they  fear of paying two rain-makers for each order-packer.