Other options I've used are to create some sort of "karma points," making only especially good characters eligible for raising based on their positive actions. This resulted in exactly one raised character over the last decade in my D&D campaigns. I've also removed Resurrection and moved Raise Dead to its spot as a high level spell. In my campaign, there were only three clerics who could cast Raise Dead, now a 9th level spell, and it required a literal trip to the underworld. Who is going to do that for you?
Another option is to make the party jump through hoops. Perhaps there's a special place or a special artifact that will allow this very difficult thing to happen. Raise the Dead is a Sword & Sorcery product that's all about that. I've read it and planned to use it, but never got the opportunity. The description of the book says:
Now You Must Pay the Price Raise the Dead turns death into a chance for adventure! Occasionally, a player character dies. This DM Utility product contains four thrilling quests designed to bring a fallen hero back to life. It includes options for non-good aligned characters and other 'difficult to raise' characters such as druids, rangers and non-humans. This book also allows interesting options for the player of the deceased character.
The down side to a special quest is that the party is already on a special quest, your adventure! How annoying for you if they put it on hold to spend three sessions to find the magic amulet to raise Dave the Thief. Dave, let it go, go into the light.
4th Edition tweaks Raise Dead slightly from what we know, but mostly to change its flavor. Raise Dead is tied to having a destiny. The characters in the game, because they're on this special path, clearly have a destiny that requires their return from the after life. The main villains also have a destiny, as destiny is agnostic and doesn't care if you're good or bad. Kings and the like have a destiny, but in a slight twist of logic, their destiny may have been to die in the way they did. Huh. I'm not so sure about that part, but the idea here is that it tries to answer the question of why everyone who can afford it isn't raised. However, it's only a facade and doesn't change the fact that characters can be raised without much effort. This changes nothing for me, but I'm reluctant to house rule it once again before the books are even printed.
Monte Cook had the same issues of a believable reality when designing D&D 3, and it shows up in his Ptolus book and his design diaries. In Ptolus, there are diseases that are magical in origin and are immune to curing. There are insanities that resist magic as well, driving mad a cleric who tries to remove them. Once you start in with a magical world, you sometimes need magical results to common problems. In some fantasy novels, for example, assassins may use special weapons that destroy your soul if you're assassinated with them. Cool, a magical solution for a magical problem.
It's not surprising then that Monte Cook's new Book of Experimental Might makes raising dead a special event. I'm waiting for my LULU copy of BoXM, when I'll have more details. Pathfinder RPG sidesteps the issue and makes no changes to Raise Dead. I guess Dave the Thief still has a chance.