Which Chemical Database Software Are Available? By chemical database software I mean software with similar functionalities to Instant JChem in that they have a large database of different compounds and have the basic capabilities you, or at least I expect from a chemistry software. Namely: 


Can approximate the chemical and physical characteristics of the compounds in question.
Can approximate products of reactants and their corresponding proportions. 
Can show the 2d and 3d structure of compounds in the database.
Can connect to online chemical databases like PubChem, ChemSpider, NCBI, etc.
Has a molecule editor.


I would also prefer it if it is free of charge.
A widely used database in academia and industry is ChemACX.The only one of your requirements that I don't believe it does is the product prediction.

http://www.cambridgesoft.com/Ensemble_for_Chemistry/ChemACX/Default.aspx