There is a curious thing happening in customer relations in the United States these days. The use of the response "you're welcome" seems to be getting replaced by "my pleasure."
Growing up, saying "thank you" meant getting a "you're welcome" immediately afterwards. Like "day" and "night."
When this first happens in an interaction, it's pretty disconcerting. There are certain language cues that become very ingrained in our consciousness, to the point where, if some thing different happens, it's like tripping over a mental crack in the sidewalk. If I casually use the greeting "How are you?" (or somesuch variant of the phrase), predictably I'm going to get something like "fine," "good," or (if the person I'm talking to is having an actual good day) "great!"
Sometimes that's the problem with language. We often say things and don't put a lot of meaning behind them. They are a social construct, phrases and words that we say because they are expected. Not meant in the sincerest form of the word.
When we say thank you, the purpose is that we are expressing gratitude for something someone has given or done for us. But by making the phrase so transactional and expected, we can say thank you all the live long day and it might not mean as much.
This is not a call to say "thank you" less. But it is a reminder that we all need to get a bit more purposeful with the thanks yous we do deliver. Don't just toss off the phrase and call it done. If your project has some sort of karma system in place, use that. The Fedora Project uses an IRC-channel bot that, whenever a unique user types username++, the recipient gets points in Fedora's karma system. It's simple, but it lasts, and it shows to the rest of the Fedora community that this person has been helpful.
Another way is to individualize your thank you. If someone helps you with a particularly complicated problem, point out their talent when you express gratitude. "I really like the way you…"
Also, be more mindful of public thanks. You don't have to make a production number every time someone does you a solid, but for the significant achievements, mention the accomplishment to other people. Putting gratitude in the public eye delivers sincerity in a bigger way.
As with all things, maintain a balance. Overdoing it will just cheapen the action and make the whole thing pro forma and transactional–the very thing you are trying to avoid.
Image by JC Awe, under Creative Commons Attribution 2.0 Generic (CC BY 2.0) license.