I know it says all time favourite, but I've got too many and also there are so many other Anime and Manga out there that it's nearly impossible to have only one favourite.
Lets begin...
(These are a few of my favourite in no particular order or rank LoL)
School Rumble - Harima Kenji (He could be my one and only Hero)
Bleach - kurosaki Ichigo, Rukia, Kon, Nelliel
Samurai Champloo - Fuu, Mugen and Jin
Naruto - Rock Lee, Hinata and of course Naruto
Code Geass - Lelouch Lamperouge, Kallen Stadfeld and C.C.(for stickin with a brother till the end)
Eureka Seven - Renton
Tenjho Tenge - The Natsume Sisters and Souichiro Nagi
Soul Eater - Black Star
Fairytail - Erza Scarlett
One Piece - Roronoa Zoro, Luffy and Ussop
Air Gear - Ikki, SIMCA and Ringo
Hitman Reborn! - Reborn, Lambo (Big n Small)
Eyeshield 21 - Sena, Kurita and Hiruma
Gundam Seed - Kira Yamato and Athrun Zala
Tengen Toppa - Yoko
Tokyo Underground - Rumina Asagi and Ruri Sarasa
Well thats about all I can think of off the top o my head, but believe me there are way more...