I was just thinking of names and their possible anagrams... This is just for fun, I don't think that these are hidden secrets, just funny or interesting...
Charlie Pace- Peach Eclair ;)
Daniel Faraday- Anal Dead Fairy (I like Daniel but too funny not to include), A final dead ray,
Miles Straume- Mutes Realism
Boone Carlyle- A Rebel Colony
Richard Alpert- Retard Pal Rich (sorry Richard fans), Rare Part Child
Ethan Rom- Other Man
Kate Austen- Taste a Nuke
Hugo Reyes- Heroes Guy, Oh Seer Guy (Seeing the dead!), Shore Guy
You can get AJIRA out of Sayid Jarrah
Sun Kwon- Known Us Sun Hwa Kwon- Wow Sun Ankh (just trying to make something with ANKH!)
Jin Soo Kwon- O Join Kwons (get them back together!) or So Join Kwon.
Ji Yeon Kwon- Enjoy, I Know!, Woken in Joy
Desmond Hume- Hmm, Do Us Need?
Aaron Littleton- Lantern alit too
Elizabeth Smith (Libby)- Hate Blitzes Him, Ahh Blitzes Time, Blaze Me This Hit (Libby's secret drug addiction led her to the psych ward ;) -seriously... joking.
Peter Avellino (Sayid shot him on the golf course)- Alien plot veer
Charlotte Lewis- Celestial Worth
Benjamin Linus- Blame in Jin Sun, I blame Sun -n- Jin, Ninja Nimble Us
Pierre Chang- Recharge Pin, Can He regrip
OK enough wasting time...