Is there a best tool for use to load up data and do a comparison large sets of data apart from Excel in a customizable way?
Talend Open Studio for Data Quality is a great tool for data comparison, data validation and lot of other data testing features. You can upload data from different type of sources into it and perform the checks.
But note that it is comparatively complex tool to begin with, so learning curve could be an important factor while choosing it.
Another tool that is very popular is RedGate, I have used it in the past with good results: http://www.red-gate.com/products/
How you are going to take data? Are you going to dumb the data from db or any external sources.
If you want to compare table data between tables in two different databases.use below tool