I have been investigating the same question for my own line-of-business application that uses Index server, since it has been dropped from Windows Server 2012
Alas Windows search is not really the successor to Index Server, lacking interfaces for configuring multiple catalogs, amongst other things. The interface provided is oriented toward searching all the content on a workstation, rather than a platform for content searching on a line of business app.
MS Search Server is more complex to set up than Index server, and oriented toward URL crawling rather than file searching. The versions I looked at did not seem to provide the flexible API of Index Server.
The Lucene.Net toolkit is attractive, but you have to write a lot of infrastructure around it to make it work. It is not an out-of-the-box tool in the way Index Server was. It does offer the potential of a much better integrated solution than you could achieve with index server if you have the time to invest.
dtSearch is quite close to the concept of Index Server, but costs significant money. This is probably the easiest option if it is cost-effective.
Index Server was the unsung hero the original Cairo project. Perhaps some of the underlying engine lives on in the 'successor' products, but it is sad to lose it from Windows Server 2012. Microsoft have been very effective in recent years in monetizing their server business. I feel this may be one of the causalities of that strategy.