I added Word Replacer to a relatively fresh install of WP 3.0.4 with MU active and about ten other plugins (including domain mapping). I met with two issues though.
One is that the plugin needs to check that the correct form is being submitted when attempting to apply changes. I had to make the $_POST conditional verify that one of the word replacer variables was specifically set (not null) as a crutch so it wouldn't spit out an (occasionally fatal) error when I submitted an unrelated plugin's form.
Second, if the plugin is "network activated" instead of individually activated, it will not let me save the replacements on any site other than the primary. I skipped on tweaking the code for a fix on this issue, but I believe it is worth looking over at some point.