Mine is Latios...Even though he is impossible to catch without a masterball. I picked up my Emerald game again and ran into him THREE times in thirty minutes in Fortree. ( ̄□ ̄;) Playing hard to get..
__________________
"QUICK! CALL AN AMBERLAMPS!!"
(゚ー゚)..(。_。)..( ゚,_ゝ゚) "Amber..lamps..?"
My favorite legendary for Generation III is easily Kyogre. I had always challenged my brother with battles between the two Kyogre and Groudon, and with the typing advantage (and knowing nothing about EVing/competitive play back then) I had always won. :D; There are some other legendaries like Jirachi, Latios and Latias that I like as well though.
Groudon is my favorite legendary in general and one of my favorite Pokemon, just because it looks like a dinosaur and Ruby was my first Pokemon game haha.
Rayquaza is definitely my favourite of them all, wish I could catch a shiny it looks so wickedly awesome.
Latias is also super cool, haven't caught a Latios yet though, am leaving that capturing it as the wandering pokemon in my second run of Emerald.
I just really wish there was a 'Legendaries battle mode in the battle frontier so they could be used for more than just trophies though. . .
My favorite is Jirachi, even though I can't capture it... It has a good type combination, it's cute, has good stats and an exclusive move, a good trait, so I really like it *-*
Latias comes in second place, for the same reason as Jirachi, but I'm not fan of roaming pokemons, they are so annoying to catch e_e