I usually read them through my Blogger Dashboard. I'll read and comment on all the most recent posts, then I'll read my top commenters and comment on their blogs, then I'll venture out into Google Reader and read the rest. I'll comment on my loyal readers and my favorite blogs first, and then I'll comment on posts that interest me... hmmm, you didn't ask about my comment habits, did you? ;-)
I follow some by subscription, others by reader and others by blogger following. I go take a quick look at everyone's updates and open those which look interesting. I read them and comment on them. Given that now I am following more than I would be willing to comment, I would probably choose about 10 blogs to comment each day in a given time, say 30 minutes to read and comment. If time is not up I might comment in more than 10.
I start at the top, and make time at least once a day to go through, at the very least. Also, by keeping in contact on Twitter and Facebook, I can usually get a head start by their posting of links to posts, or important things they've written, since I connect with my favorite bloggers and writers there, too.
Sometimes it's overwhelming, but you know what? If you can't clear your reader everyday, don't. Just be sure to catch up when you can, and do what you can, when you can. That's all you can really ask of yourself, you know?
Honestly I admit that I have a really hard time with keeping up with ALL of the blogs I follow. So I try to at least view my Google Friend Connect Reading List under my dashboard where it shows the blogs I'm following. I'm usually drawn to titles of posts and then when I see one that peaks my interest a bit I check it out. But even if some don't peak my interest I'll still try to visit them from time to time, but it's nearly impossible to do daily or even every other, other day as being a mom we all have kids and responsibilities and can't very well sit at the computer all day and night, ya know? I also have subscribed to get emails sent to me from some blogs and I'll view those too, which seems to help me keep on with them.
But again, it is hard to stay on top of and I have fallen a bit behind from time to time. All I say is that I just try to do the best I can to keep up. I know other's also have this problems too; no doubt because I know a lot of people follow me and I only have about 2 or 3 regulars who comment on my site, but I don't judge anyone over this, as I too haven't been the best at keeping up. Maybe if I were an octopus and had 8 arms to do everything than life would feel so much easier in this area. Wishful thinking 'eh?
I use google reader and sort by daily reads, weekly reads and monthly reads. I start with my daily each morning and work my way though. My monthly ones are for when I have extra time or I try to at least stop by once a month. I wish I could do more but there is only so much time in a day :)