I'm not aware of any lists having specific rules about using ssi or php includes. That is providing of course your server is fast enough to 'include' those includes seemlessly. And that your server is properly configured to parse the pages to .html instead of .php or .shtml.
You're right in that link lists don't like dynamic pages for a variety of reasons. However, if your server is fast enough and correctly configured...there's no way a reviewer would even know you're using includes.
When doing free sites, I have a series of .txt files. I submit to 48 link sites...16 recips per page...so three recip tables per niche. Similar to Viper, I simply name those .txt files as needed, ie..
amateur.txt
amateur2.txt
amateur3.txt
Then insert the include into the index page html...
<!--#include virtual="/ssifolder/niche.txt" -->
Once the intitial harvesting of recips and layout of the tables is done (tedious, but necessary), the above method works quite well
I'm not aware of, nor would I endorse any software that somehow harvests and/or creates recip tables automatically. But then, as a reviewer I've seen some damn ugly recip tables so my opinion is probably biased in that respect
