Tabula is a tool for "liberating data tables trapped inside pdf files." It extracts data tables from pdf documents to comma- or tab-separated value formats (CSV or TSV). Note that this only works for text-based PDFs, not scanned documents (which are basically images). Tabula runs within your browser; just upload your files and extract. Data can be corrected before downloading.
UnScanIt & UnScanIt Gel
UnScanIt allows you to extract (x,y) data values from scanned images of charts or graphs. UnScanIt Gel includes the basic UnScanIt functions, but also allows you to quantify any type of electrophoretic gel, from Western blots to TLC.
OpenRefine (formerly Google Refine) is a desktop application that can help you clean up messy or inconsistent data by helping you locate those inconsistencies and providing easy ways to fix them. It can also help you transform your data and extend it with web services. All editing operations are tracked, allowing you to roll back to previous versions.
Projects software from Digital Science is designed to help you manage your research data, improve efficiency, save time, and be better organized. It is NOT an electronic notebook; it's a simple interface designed to help you keep track of things a little more efficiently. The software includes integration with figshare collaborative spaces so that you can invite others to share your research online.
This web site also contains information about other types of helpful tools: