When deploying Search Applications, the choice over which platform to choose is not as clear. Autonomy's focus is on flexibility So IDOL provides a toolkit that can be used to solve complex search problems. Naturally higher complexity, makes it more difficult to setup and maintain resulting in a higher TCO. But to be fair, this can be justified in circumstances where search is core business. Microsoft FAST has been successfully leveraged to build Search Applications particularly in the area of e-Commerce, so an organization must carefully assess the pros and cons of each platform depending on their goals to make the right choice.
The last thing I'd like to mention is I found it interesting that both Microsoft and Autonomy rely heavily on partners to deploy their software. But oddly enough I couldn't find any ISV partners for Autonomy. Microsoft will often leave features and functionality to ISVs as a partner opportunity. As an example, Autonomy is known for the large number of search connectors that they have, whereas Microsoft has comparatively few. But Microsoft partners like BA Insight fill this gap by providing over 30 connectors to the most common ERP, CRM, ECM, and Messaging Apps. More on that here: http://www.bainsight.com/sharepoint-fast-search-connectors/Pages/default.aspx To get more information, download this Autonomy and Microsoft Enterprise Search Product Comparison document.