A number of databases including SciFinder now enable you to search using a graphical interface to input a chemical structure.
Chemspider supports the use of chemical structures as search queries. You can draw a structure using the editor, or convert a structure from an identifier. Chemspider also enables substructure and similarity searching.
This step-by-step guide also provides a useful overview of searching by structure in Chemspider.
PubChem Structure Search has a drawing editor and you can also search by uploading a structure file.