BPBible is a free, flexible Bible Study tool designed for ease of use. The program has many of the features you would expect including bible, commentary, and dictionary support, search, scripture tooltips, etc. BPBible uses a proximity-based search, rather than just a verse-based search. This means that a search can cross-verse boundaries, giving a more natural search. It also supports regular expressions and phrases.
BPBible can read many modules. The main module repository is the CrossWire SWORD Modules repository.