The main two are Groudon and Rayquza.
It depends on what you mean with "rare".
a few
you can get feebas on route 119 very rare
You can find it in Route 129 but it is rare.
route 102 they are rare
n e where
you can find groudon, mew, mewtoo, rayquaza, kyogre...
fuji yama shushi
In the weeds were you can find when you dive (rare)
In Ruby, Sapphire and Emerald on Route 116 and are rare.
Route 119. They are moderately rare, though.
You can find a lightball on wild Pikachu, but it is very rare.