The big one is that Lisphp is an interpreter while Pharen is a compiler. Lisphp takes source code and just runs it, which means that it's lisp code running on Lisphp, which in turn is running on the PHP interpreter.

Pharen generates regular PHP source files that you can then throw wherever PHP works.

How do they compare performance wise? I've tried some 'toy' lisp programs in Lisphp and was pretty disappointed at the speed, does Pharen fare better in this respect?

I haven't done any real benchmarks, but theoretically Pharen would have at least the same order of magnitude performance as regular PHP. The main things slowing it down is the memory overhead needed for using lexical scope.