Pedigree Plus - Database of over 140,000 pedigrees plus features like hypothetical matings, six generation pedigrees, and more. Also available in a cheaper version with no database, you build your own.
Precision Pedigrees - Offers Stud2000 software. You can download the entire program and run it without any restrictions during the demo period.
Richard Ulbrich's Peerage - Richard Ulbrich has compiled a mosterous collection of notes on over 40,000 of the most prominent thoroughbreds in history. While his database may be a bit on the small side, the comments more than make up for the missing information and all of the major lines are included.
Software Reviews - Reviews of all the major pedigree software products on the market.
Tesio Power - Generally considered to be the best breeding & pedigree analysis software on the market. While expensive, there's a reason, Tesio Power is packed with impressive features and includes a fairly comprehensive database.