PDF is pretty much ubiquitous. You can write to PDFs that are fully searchable with PDFCreator ( http://sector7g.wurzel6.de/pdfcreator/index_en.htm ). I am amazed at how well this software works and it is FREE and OPEN SOURCE.
If you write to JPEGs or PNG you won't be able to search for text.
I prefer scanning at 300dpi, black and white. It makes all the difference in the world if you ever want to print out a copy. The file size isn't all that much larger. Besides, you can get a 160 gig hard drive for less than $100 these days. Don't skimp on quality now. Not only that, but PDFs will compress the data for you nicely.
For things like professional certifications, I'll usually do color.
I usually shred my docs after scanning them - save the important ones and certifications. The laws are changing. Electronic records are a very attractive alternative to paper.