When it comes to things like spirituality and religion, which are inherently unprovable, the sincerity and social impact of the beliefs is the only thing you can really base your judgment on.
Let me explain. You have two preachers. One that walks the walk as well as talking the talk. He (or she) tries to live according to the teachings of their belief structure. While I may not agree with the actual beliefs, I do respect the conviction of those beliefs. The other preacher takes drugs, steals from the church, and is, oh, say, caught in a hotel room doing ecstasy off the abs of a gay prostitute. (Ted Haggard anyone?) This preacher then denies, denies, denies before spending a weekend in "counselling" before announcing he is totally cured and everyone should forgive and forget and besides, doing X off the stomache of a gay prostitute isn't a gay act, anyway, right? Now THAT guy, even though he claims many of the same beliefs as the first preacher, that guy is full of shit and I have no respect for his beliefs, even though they are supposedly the same beliefs as the first guy.
With the first guy I will be polite and considerate of his beliefs and the differences between those and my own. With the second guy? Probably not so much.
As for the social impact, I can explain it like this. I believe Buddhists to be wrong (and I base this on a lot of knowledge, I was Buddhist myself for a while), but I have a lot of respect and admiration for their beliefs. They do not try to force their beliefs on others. The core of the belief structure, while as irrational as any other religion, is essentially altruistic and compassionate. I think they take things a bit too far, say, in dietary and a few other aspects, but the belief structure is, on the whole, harmless and positive.
I generally like a sincere Buddhist. They tend to be good people who hold culturally and socially positive beliefs. As my granddad would say. "Tha's good neighbors."
Scientology, on the other hand, aggressively recruits for the sole purpose of acquiring money and power. The church blatantly abuses and threatens the faithful. They seek to enforce their "rights" and beliefs on all those around them while deeply obfuscating the actual nature of those rights and beliefs. Scientology is selfish, destructive, and hateful.
I generally can't stand Scientologists. They tend to be arrogant, disdainful, secretive people who are following a belief structure that is damaging and destructive to the culture and society. Granddad would dismiss them as "sticky basta'ds."
See? The sincerity of the beliefs and the social impact of their implication is about the only thing you can base your respect on, since the veracity of the beliefs can not be proven.