I've defined "spirituality" as the quest for the noumenous and/or the trascendental, and "religion" as the institutionalized or organized expression of spirituality. Some people may find that oxymoronic, like trying to "catch a snark with a railway share," (Hunting of the Snark) but it's a definition I can work with.
There are some abuses of religion that divorce it from spirituality altogether. These may be superstitious and commercial, like the medieval sale of indulgences (recently secularized and updated as "carbon credits") or like the mass market for amulets in Thailand. But I can't get too upset about that, it's almost like the Nigerian scam letters, if you're foolish and greedy enough to believe in it, you're not a very sympathetic victim. The worst harm comes from the disrepute it brings to genuine expressions of religion, but I hope most people can discern the difference.
A much graver offence against the spirit of religion is when it religious rhetoric is used to justify war. No major religion has completely escaped this blemish; Buddhists sometimes boast that we've never had a war fought in our name, but that claim is historically dubious to say the least. We should face up honestly to the misuse of Buddhism by some Zen priests in 1930's Japan and by some Theravada monks in contemporary Sri Lanka. If we're not honest about that, we can't fairly point the finger when adherents of other relgions go down the same dark path.
A very dangerous aspect of the manifestation of Holy War is going on in Iraq. We hear a lot about Islamic extremists, but less about their mirror image found in the American forces. There are many stories coming out about the penetration of extreme dominionist christians in the US armed forces. Dominionists are a very polticized wing of the fundamentalist movement, who believe that America should be transformed into a theocratic state. It appears that the Air Force may be particularly full of these people. (See this article from the progressive Jewish site, Tikkun.) There is also the scary rise of the mercenary army Blackwater, which is run by Dominionists.
Now the Army has authorized a tour of US Forces in Iraq by the "Left-Behind" group to promote and distribute a video game based on a post-raptured New York where Christian soldiers seek to convert the heathens and kill those who can't be saved any other way. "Left-Behind" refers to a series of novels based on the Book of Revelations. The writing is pedestrian, the theology absurd and there is lots of righteous killing of the unsaved throughout. But they sell really well. They've already made a film, and now fans can download the game and destroy the ungodly hordes in comfort of their own homes.
Or they can go to Iraq and do it for real.