I think my conversion to recomending canned software for FMEAs, as much as I HATE canned software, is from the companies I have been in which did FMEAs in Excel. While I have seen some good FMEAs in Excel, I have seen more horrors. The root cause of most of the 'problems' was people doing them didn't really understand how to do an FMEA. Canned software somewhat forces the correct way to do them in the same way one can learn statistics by using a statistical analysis program.
If the people really know what they're doing, I have no problem with Excel.
As a secondary comment, if you're doing FMEAs you're probably automotive. In that case there is some pretty good software which does the whole shebang - FMEA - Control Plan - Process Flow Diagram --> all linked.
One aspect to consider is length, as well. I've seen 1 page FMEAs and I've seen 300 page FMEAs. If you're looking at 50+ pages, I'd be looking at canned software.
You can download a free excel based fmea program at http://www.fmeainfocentre.com/downlaod_area.htm
The real problem with independent programs, those that do not connect the CP, Flow chart and FMEA is that you have to work hard to ensure the consistency of numbering etc.