I started playing my Ruby one day, and found that my Groudon and Rayquaza of 90ish levels had been replaced by a Zigzagoon and a Corphish with my friend's ID.
The weird thing is, neither of us had any recollection of trading them. I let him keep them, and bugged my other friend to give me his.
Also, my Ruby version randomly crapped out on me one day and wouldn't load my save file, with the only option being to start a new game. I turned it off, and when I next turned it on, my save was back.
Really, the only other thing (again on Ruby) is that I was freaked out when I saw my friend's Battle Tower team appear when I went through.