If someone bidding against you is using a snipe site, they can still only win by having a higher maximum bid than you do.
I don't use a snipe site, but I manually hit the "confirm bid," when it shows 3 seconds. But if my "max bid" is only $8 and someone else's is $15, I'm not going to win regardless of entering it manually or using a snipe site. So make sure your max bid REALLY is your max.
If you see the auction close for one increment higher than yours and that makes you upset, then your max bid wasn't really your max. But remember that just because it closed at one bid increment more, that it didn't mean that the other person's max wouldn't have been $5, $10, or $50 more than yours. You could have bid that extra $1 and still would have been outbid by one bid increment.
The snipe sites help so you don't have to "babysit" your auctions, especially if you have a couple closing within seconds of each other. But if you aren't willing to pay more than the other guy, sniping isn't going to get you much.