I've only used a Source brand hydration bladder, which came with my kelty hydration pack (excellent deal for only $20), They're also available direct from Source and probably come with other brands of hydro packs.

I've left water in the bladder for weeks, in hot and often dirty conditions, and I've never had a problem with bad tasting water. I usually use filtered water, but I have used unfiltered water a bunch of times as well. I also never use anything other than water in it, if you that might be part of the problem.
I recently got the camelbak brush kit and now I clean it regularly, but for the first few months after I bought the pack I rarely cleaned it and even then just rinsed it with soapy water.

The bladder and tube both have some kind of anti-microbial coating, which is probably why I've never had a a problem.

FYI these are made in Israel, and I've heard that there used in the Isreali military(this is uncomfirmed, but highly likely for obvious reasons). Anyway I figure that people who live their whole lives in a desert know a thing or 2 about hydration.

I don't mean to sound like a salesman, I'm just a very satisfied customer recomending a good product.