I'd say the advantages of the CD-ROM's are "availability" (independent of whether the internet or your phone lines are up, or working slowly. The CD-ROM is very quick. Also, the Guild Press CD-ROM gives you other value-added materials (see earlier post for their contents).
The disadvantage, possibly, is some slight error rate, plus you have to pay for the thing. The Cornell University "Making of America" site provides a digitized image of the actual pages, directly out of the OR, whereas the CD-ROM is a "transcribed" version of the text. The image and transcriptions are supposed to match exactly, but technology is not absolutely perfect. The eHistory site is also a "transcribed" version of the OR. Searching in both sites is possible, but again the ease of use varies according to the determination of the user. (And, when I say 'transcribed', I mean the original page images have been digitized and then electronically transformed into text. Here there is a possibility of electronic error, in both the eHistory site, and the Guild Press CD-ROM's)