methods or products to query objects?

Have you looked at http://en.wikipedia.org/wiki/Apache_Solr? It's a search engine in a box. Although maybe that is too high level for what you want.

I'm really not sure I get your situation, but are you looking for something like an http://en.wikipedia.org/wiki/XML_database you can transform the data into and hit with http://www.w3schools.com/xpath/xpath_examples.asp or http://www.w3schools.com/xquery/default.asp? Or maybe you are a candidate for a more popular NoSQL solution like, for example, http://www.mongodb.org. Its query language, like its data, is just Javascript, so it's pretty natural for most web developers to work with. Maybe also look at http://htsql.org/doc/showcase.html as a model for allowing end users to do semi-arbitrary queries of the relational data. Insofar as it's RESTful, maybe you can figure out how to extend it to handle your other data using an XPath-like syntax.

It depends what you mean by "and other parts are not." Are they unstructured documents you need to do full-text indexes on? Are they semi-structured documents that you want to extract some structured information from? Are they structured but just not in a relational form? I came in here to recommend HTSQL - I haven't used it, but we looked at it briefly for a similar situation. Especially if you have some dev time to dedicate, it could work well as part of a system for something like this. MeFi Mail me if you still have questions - I do very similar stuff for work :)

Sounds like you want to write some database views over your data, to hide the complexities.

Nothing is full text. Some of the data is relational some of it is not. It is all in an SQL database but there data that needs to be extracted trough programming because the authors chose not to use the relational model (I don't know why). I could extract this through programs and normalize the data into a different database but that would be a lot of work and I still would not have something end users could use easily. The reason coding converting this data to objects appeals to me is that I could make it fit into an object model quite elegantly. I have spent time with google and wikipedia and have not yet seen a way (for end users) to query objects easily and wonder if there is something that I am missing or if I am asking the wrong questions. Thanks

The reason coding converting this data to objects appeals to me is that I could make it fit into an object model quite elegantly. And the reason converting the data to objects won't work is because your data isn't well-normalized. You need to get your house in order first. First normalize your data. Then read up on http://en.wikipedia.org/wiki/Object-relational_mapping (ORM) which is precisely what you're talking about. In the Java world we use http://www.hibernate.org/ (NHibernate in the .NET world).

Haven't used them myself, but you may want to take a look at some of the open source OLAP tools out there, like http://en.wikipedia.org/wiki/Mondrian_OLAP_server or http://sourceforge.net/projects/cubulus/.

if you don't want to drive yourself insane, normalize your data, then the tools become a lot easier.

http://en.wikipedia.org/wiki/Garbage_In,_Garbage_Out. Normalize your data.