Not in any particular order, I'd say my top 10 cutest Pokemon out of HeartGold and SoulSilver are:
Teddiursa, Cyndaquil, Pichu, Togepi, Ledyba, Wooper, Bellossom, Shuckle, Swinub and Marill.
I guess it's all down to personal opinion, though. Unlike some of the other posters in this thread, I've always thought Mareep and Phanpy were kind of boring, yet I have something like Ledyba on my list.