The system I’ve come to use is a Platypus 2L bladder with a sawyer inline filter attached to the hose to filter the water while I drink it. I fill the bladder with “dirty” water, and don’t have to deal with a pump. It's very important that once your bag is dirty, that you remember that. Don't go drinking straight out of the bag. Mark it with red marker or a piece of red tape to help you rememer. The system can also be used as a “gravity fed” filter to fill water bottles or pots for boiling water for freeze dried meals. This system works very well so long as the water quality is good and the water isn’t muddy which is generally the case in mountainous areas during backpacking season.
The major benefit to a bladder is that you can drink from the hose whenever you like without the need to reach for a bottle, or take off your pack to get a drink. This of course helps you stay hydrated with the ease of drinking.
If you would prefer to pump your water, there are a couple companies that make lightweight pump filters, katadyn and msr, and several companies that make filter bottles.
These filters are a little more dependable if you're hiking in an area where the water sources aren't that abundant. If you're likely to be filtering your water out of a small puddle or murky spring, this is the route to go. These filters will be able to handle more sediment/gunk in the water.
With this, you should be able to connect straight to the bladder without even having to remove it from your pack. Just take the mouthpiece of of the bladder and into the output connection on the filter.