This will be Batman Begins spoiler-heavy, so I'd skip this if for some reason you haven't seen the movie.
Sure, Ra's al Ghul appeared to die at the end of Batman Begins, but there are a couple different ways he could return. In the comic books, Ra's is "The Demon's Head," the leader of the League of Assassins, who has lived at least 600 years, thanks to his knowledge of alchemy and use of life-restoring Lazarus Pits. So even an apparently fatal train accident wouldn't be a problem to the comic book Ra's, who would merely have to be brought to one of the pits. But dunking a corpse into glowing green goo to bring it back to life is a bit of a stretch for the tone of these movies.
The more likely option is that Ra's al Ghul isn't a single man but a title. When Ken Watanabe's character, who we believed to be Ra's al Ghul, died and was replaced by a different man claiming to be Ra's, I assumed that was the case. That the death of the real Ra's could result in a new man taking over the organization, inheriting the title of Ra's al Ghul. And it could still be done that way. (image stolen from Dave Johnson)
Pros: He's a villain that worked well in the first movie. That the organization had been around long enough to take down Rome would imply that one foiled plot and the death of one man wouldn't be enough to stop the League of Shadows anyway.
Cons: People get more excited by seeing different bad guys, and tying the plot so closely to the first movie might be a bad idea given how much more popular The Dark Knight has been.
How I'd do it: Still determined to destroy the corrupt Gotham City, the League of Shadows returns, hoping to take advantage of Batman's weakness while he's pursued by the police. Stealing an idea from Bane, they find as many crazies as possible and let them loose on Gotham City, then try to take the whole city down with whatever their new plan is while Batman's distracted.
Casting Guesses:Christopher Eccleston is awesome in a Liam Neeson-like way, or Mark Sheppard if you want to keep him English, but it might be best to have the replacement Ra's go a different way. Avery Brooks hasn't done movies for a while, but he could really nail that part. I don't know why I just named three guys I know best from Science Fiction TV shows, but they could all play the part well.
Verdict: If the League of Shadows does comes back, Talia should be running it, since a new character would be more exciting than the return of Ra's, and she also fills the need for a new love interest.
After The Scarecrow, Ra's Al Ghul, The Joker, and Two-Face, who should be Batman's next enemy in the Batman Begins/The Dark Knight series? Well, as of now we know that Tom Hardy will play Bane and Anne Hathaway will play Catwoman.
Check out the master list for all the villains covered. I've pretty much run out by now. Obviously, there are more Batman villains, but not any of significance that I know of. As of February 2009, no one is confirmed as a villain. Not the Johnny Depp Riddler, not Phillip Seymour Hoffman Penguin, nobody.