As stated many times, the application I primarily use is
FontExpert. It works with unmodified fonts only but does come with a large supplied database and a database generator for adding in your own fonts. The best solution for dealing with modified fonts is to bring Photoshop into the mix and to stretch, squeeze, rotate and unslant to attempt to restore the text sample to the unmodified version it started out as.
I like a product called
TypoGraf for doing manual comparisons although many font managers work in the same way. Finally, I like MyFonts.com for its fair prices, large selection, search engine and ability to type in your own text string.
Having a good sized, organized type library is a big plus and learning all one can about typography is a requirement to have reasonable success IDing fonts.
There is also a type ID feature in the autotracing application
Imagaro Z. Like FontExpert it allows you to add in your own fonts and also will attempt to stretch or squeeze its database characters to fit your sample. I own a copy and prefer to use FontExpert for its speed. By comparison, I find Imagaro Z takes longer to use and is not as accurate.