All of the stones I've purchased, I've gotten on ebay. I know that's probably not the most traditional way many people would choose to get their stones. But, so far, I've been pretty lucky and everything seems genuine. Usually the way I can tell if a stone is the real thing is by holding it in my hand right against my chest, and I can sometimes feel my heart quickening as I do this. Or I'll get a tingling in my forehead. It usually takes a little less than a minute for me to feel something. Sometimes I'll get a bit of a headache or even feel a little queasy if it's a really strong stone. This next one is going to sound silly -> Or sometimes I'll actually put the stone right at my lips and I swear I can feel the energy pulsing in my head when I do that. That also takes a little less than a minute for me to feel something. I guess everybody's different in how they're able to sense the energy of certain stones.
I know that probably doesn't help, because you obviously want to know if it's real before you buy it. I usually go off of the ebay seller's feedback to see how much business they do, and how many of their customers are satisfied with what they receive. If they're selling junk, it will definitely reflect in their feedback.
I purchased some Lemurian crystals late last year. I went to pick them up at the post office and on the ride back to my apartment, I had them sitting in the front passenger seat next to me, and I got this throbbing headache all of a sudden because the energy was so strong. I've purchased a few batches of Lemurian crystals and they've done this to me everytime I've gone to get them from the post office. I carried a few of them in my pocket after I got that first batch, and I felt like I was walking around in a daydream. That's how spacey they can make you feel. They're these crazy powerful healing crystals that are supposed to connect you to your Higher Self. I've seen people on ebay selling single Lemurian crystals for outrageous amounts of money ($10-$20 for just one!). If you decide to purchase some, there are some sellers in China who sell them in batches (you can get quite a few for a reasonable price). The only problem is that shipping will take about 2-3 weeks longer, but it's worth it. You can then spread them around your home if you feel like it.
As far as ebay goes, you mainly have to be careful of people who are selling the real thing but are overcharging for it. I've come across that more than anything. Compare prices between several sellers before you make a purchase, to make sure you're getting the best deal.
There was this one time that I didn't receive the right stone. About 6 months back, I purchased some Tourmaline tumbled stones, but this one seller sent me a few Apache Tears in the mix instead of all Tourmaline. I gave her the benefit of the doubt and figured she just made an honest mistake because they're both very dark colored stones. But if you hold Apache Tear up to a light, you can see right thru it like Smoky Quartz. But everything else I've purchased from her has been the real thing, so I didn't say anything. Maybe the Universe decided that I needed some Apache Tears and that's why the mix-up happened. :-)
Another powerful stone is something called Moldavite. Right after I purchased that piece of Bismuth, I bought a piece of Moldavite. It's crazy powerful. It gave me a headache for the first day or two and I also felt a little queasy because it was so strong. But that went away after I had gotten used to its energy. I think the Moldavite may have opened me up to being more sensitive to other crystals, because that's something new that I've been experiencing within the last year. My crystal spheres never even affected me to that degree. But you have to be careful because there are quite a few people on ebay selling fake Moldavite. The fake stuff looks like a molten Heineken bottle and looks way too glassy to be the real thing. I got lucky and found this one guy who is in New York who sells real Moldavite. I'm in Dallas and he's in New York, so I assure you I have no affiliation with him. If you want, I can private message you his ebay user id. I don't want to post it out here and then get in trouble for promoting someone's ebay business that I don't even have an affiliation with. I've also purchased some Herkimer Diamonds from him that were also the real thing.
So far, the only thing I've seen people try to fake on ebay is the Moldavite because it's in such high demand because it's so scarce. I think you're relatively safe with purchasing most everything else.
Lura, if you have some specific stones you're looking for, I can let you know certain sellers on ebay that I've dealt with, who I know might have what you're looking for. Or I can send you a list of sellers I've purchased from, who I know sell genuine items. Just let me know. :-)