As stated before, I have many favorite legendaries.
For Generation One, Articuno and Mew reign supreme - Mew is adorable, and Articuno is the only legendary bird that actually looks somewhat majestic.
For Generation Two, Lugia, Suicune and Raikou - Lugia appeals to me design-wise (I quite appreciate the streamlined draco-cetacean-avian form) and I enjoyed its roles in PokeMon the Movie 2000 (as well as the look into their pods in the anime). Suicune is elegant and graceful and Raikou not only radiates power but is also blatantly based on a Sabertooth Cat, and those pwn hard. XD
For Generation Three, I'm fond of the Latis, but my top favorite is Deoxys - mostly because of the sheerly awesome alternative biology behind the thing... and the whole DNA helix thing. I have a strange connection with it - it is perhaps my favorite legend overall, with one exception which I shall mention later.
Gen 4 introduced a whole clustereff of legends, and only a few out of which I find appealing. Dialga is probably the top candidate for Exhibit A, followed by Giratina and Shaymin (both formes). I have a vague appreciation for Darkrai as the poor thing is an eternal underdog, tormented by its own ability. Also, it's the goddamn batman. and anyone who thinks differently, GET OUT. (Ye gods, that movie was so atrociously dubbed. XD)
As far as Gen 5 goes, Virizion is my top favorite, with Reshiram, Zekrom and Kyurem in the second place bracket.
Generation 6, thankfully, has also trimmed its number of legendaries. I quite like Xerneas and Yveltal and am wholly neutral on the new event legends. However, my true favorite of this generation - and one of my two favorite legends overall - is definitely Zygarde. Gorgeous alien serpent that is truly worthy of the title 'The Watcher in the Depths' - and even though its recently added new forms are nothing to write home about design-ways, its nature as an ecosystem-monitor compound being and the lore behind it make me love it even more.
Edit/update done.