I prefer the flavor of red, ripe jalapenos over green ones. They have always tasted much sweeter to me when red. In my opinion, the heat is slightly more when they are red. Basically, it all depends on personal preference and what flavor you are looking for. Hope that answers your question.
The red ones taste sweeter and might have a little more heat. I used to always eat them green until I discovered on this site that many folks here at THP preferred them red. I tried that and immediately noticed the difference.
I'm also with the red crowd here. Sweeter and spicier in my opinion. Plus I can buy truckloads of green Jalapenos here all day long, but red ones are rare to see available so I consider them a treat. Also, if you ever want to make your own chipotle you'll need them red.
Tabasco is the only variety that I would even consider picking unripe. I always pick my jalapenos red. I have tried a green Bhut (or Naga?) or two and I did like the flavor, but I'm not sure I'd do it again. They're like a million times hotter fully red-ripe.
Reds have a more sweet peppery taste to them and are somewhat hotter. greens have a very green, grassy flavor to them, but if you pick them right before they ripen they are quite hot and tasty too. it's a matter of personal choice.
I personally like them green better. in salads, roasted, poppers etc.
Before you give up on the green.... Make sure you try them roasted. Try them with some steak. Roasting really brings out the green flavor. I like red also, but sometimes they are just too sweet. Overall, I prefer green.
Last night I gave a chile-loving relative of mine a red ripe Biker Billy jalapeno straight from the plant. After one bite, he had the most pleased look on his face. He had no idea of the difference between red and green. Dude was in heaven...