Note that these comments are based on what is currently available in the current versions of Paup (more Paup 3.1.1 rather than Paup*) and MacClade that I've been using -- not the published standard. I can get the version number for the MacClade that I've been using, if that will help.
You can have numeric characters in your data, but they must be "hard coded," (e.g., character #4 "number of leaves" with states "1. three," "2. four," etc.
You can't put comments in your character matrix but you can put comments in your state names and character labels section.
There's not an unlimited number of states. Paup will let you have about 36 I think, but MacClade allows less. I know I had to combine some of mine to get the data set into MacClade. Practically, unless you're modeling color (which I was) this is usually equivalent to an unlimited number of states,
Character notes and illustrations only in MacClade. If you revert/convert to Paup, you loose all that information.
Taxon and character names are limited to the number of characters. If I"m not mistaken this is only true in MacClade. Either that or MacClade is once again "shorter" than Paup.
Multi-state characters -- they handle this wierd -- and differently. It used to be that they all had to be either AND or OR. And it's not even a true AND or OR type situation. It's mostly an OR, but not quite. (And I know that this is making *no* sense whatsoever!) Multiple states tend to be interpreted as uncertainty rather than polymorphism. YOu can now make that distinction, but it is still polymorphic rather than all of the above at the same time.
Inapplicable is treated as missing. There's really no other way to do it. If you have an apealout plant, all the petal characters can either be treated as "missing" or you can have an extra state "not applicable." Then, you run into the problem of that extra state providing support that otherwise might not be there.
I'm not aware of value probabilities in either Paup or MacClade.
The same situation applies to taxon notes and taxon illustrations. Those are only good in MacClade.
The typesetting markup in MacClade is only for HTML rather than typsetting.
Anyway, I hope this helps. Maybe you can get some other experiential comments about Paup and MacClade.
Susan Farmer sfarmer@goldsword.com Botany Department, University of Tennessee http://www.goldsword.com/sfarmer/Trillium