I can only tell you what I do.
I use two pieces of software. FontExpert ($149 at Smart Designs) and Typograf ($35 shareware). I also have an extensive library of fonts including everything through a couple of years ago at Adobe, most of Agfa and ITC, pretty much all of Letraset and Bitstream along with URW and Berthold. There's also a fair number of fonts from smaller foundries and cloners like Optifont and Serials.
FontExpert will allow you to do an automated comparison against its database of 25,000+ fonts. It works either when the font is not modified or you reverse the effects successfully in Photoshop of any modification. So for example, I might stretch or squeeze a scanned sample and retry it in FontExpert to see what happens. FontExpert also allows you to add your own libraries into the database. FontExpert works best with black and white samples and the characters must be on a near perfect horizontal baseline.
Typograf is very useful for matching what FontExpert misses because it is simply a very efficient way to browse you uninstalled font libraries and it allows you to type in any text you choose. So if a font has been set on an arch or modified a lot, I can usually focus on a design earmark to spot it visually within five or ten minutes.
Starting with my fonts and Typograf, I sorted my fonts into categories to reduce browsing time as well. For example, if I'm looking for a script, I can look at nothing but script faces and find a match pretty quickly.