In time order we have:
1) ספר ללאת published in 5626 by Rabbi Meir Mairim Shafit is available here and here.
2) The יפה עינים by Rabbi Aryeh Leib Yellin that appears after masechtos in the Vilna Shas (as mentioned in a comment above).
3) Some years ago, Professor Michael Sokoloff of Bar Ilan made his extensive listing מקבילות לירושלמי available in downloadable PDFs (the original URL is now a dead link and only available via the Internet Archive and is a bit slow in loading).
4) The Yerushalmi Meshulav program has links to nice PDF charts for relevant masechtos
5) As an aside, the recent ספר דרכי התלמודים is not a listing of cross references but takes a deeper dive into analyzing differences between Yerushalmi and Bavli.