SciFinder (http://hdl.library.upenn.edu/1017/50460/) searches two databases of reaction information.
CASREACT searches graphical reactions published from 1840 on, although the coverage is most comprehensive after 1975. You can search it by drawing a partial or complete reaction or link to it from an individual compound's record.
Chemical Abstracts searches the literature from 1907 on. You can search for preparations or for papers in which a particular substance is used as a reactant or reagent easily. Simply perform a substance identifier search for a name, CAS RN, formula, structure, or substructure, and click Get References. From the resulting list of substances, click Get References, and retrieve "only references associated with" preparation or reaction/reagent. If you want to find papers that prepare one substance AND use another substance as a reactant, you can do two separate searches and combine them with the "Combine Searches" feature.
Occasionally, SciFinder will tell you that a structure-based search cannot be run because the results are too general. If this happens in a CASREACT search and you do not want to limit by any of the "chemical" options (number of steps, reaction classification, etc.), try limiting your search by publication year. Search for all reactions from the past five or ten years. Then, go back and repeat your search, searching the previous ten years, the ten before that, etc. Assuming that each search yields fewer then 20,000 results, you can save each and then combine them with the Combine Searches tool to get one large answer set.
Reaxys (http://hdl.library.upenn.edu/1017/76928) is the new, Web-based interface to Beilstein and Gmelin. In addition to these two databases, it also searches a third set of substances and their reactions, the Elsevier Patent Chemistry Database. This is probably the most complete source of substances' properties and is complementary to SciFinder's CASREACT database for reactions. Patent Chemistry records include a summary of the synthetic import of the articles, which is quite useful in determining whether or not it is worth one's while to read the text of the patent.
The NIST Chemical Kinetics Database (http://hdl.library.upenn.edu/1017/11879) was created by the National Institute of Standards and Technology, a facility of the US government. The Kinetics Database gives thermal kinetic information for more than 11,000 reactions, primarily between smaller molecules. The literature is covered through early 2000. It is searchable by partial or complete reaction (text only; no structures), and you can also link to it from a compound's record in the NIST Chemistry Web Book (http://webbook.nist.gov/chemistry/)