The first thing to consider is your target audience. What sorts of blogs are the people you serve interested in? While it is a given that you should comment on blogs which are in the same niche as yourself, you will likely find that some very key connections and traffic flow can come from connecting with those outside of your niche who serve the same audience.
Using keyword searches and free tools like www.BlogCatalog.com and www.SimilarSites.com will help you build your list for consideration. Additionally, a good marketing consultant will be able to use their paid tools to build an organized target list for you - one that even ranks the blogs based on their traffic or PR ranking.
Once you have found a possible blog, the first thing to evaluate is how active it is. I recommend my clients comment on blogs that are well known with their prospective audience, which are posted to regularly - at least once weekly. There is no point commenting on a blog where the last post was made 4 months ago. No one is paying attention to it!
Also, look at how many comments the blog already receives. An active community means that people are getting involved and a high number of people will see your comments. It also makes it easier to post comments since you can pick up on what other people are saying and you can interact with or debate their points. Most often, blogs with active comments also have an engaged blogger at the helm - one who responds to comments and is more likely to be someone with whom you can forge a mutually beneficial relationship.
Of course, it is also very important to examine the content of the blog from a qualitative standpoint. Many blogs exist as pure advertising ploys (you know the ones I am talking about – blogs which have tons of advertisements and affiliate links but very little useful information.) These are the ones to avoid. You ideally want to seek out the blogs that are viewed as an authoritative voice with your target audience. You will likely also want to find blogs with which you most often agree - a blog that you would feel proud to share with your own audience. By commenting on these blogs you will associate yourself with excellent content and develop your own reputation with a quality-conscious audience.
There are many tips to help improve the quality and effectiveness of your blog commenting. I'll likely address these in a future post. The important thing now is to set a small, achievable goal to get yourself started - say, for instance, selecting 5 key blogs that you'll comment on weekly over the next 3 months. While that activity level may not set the world on fire, it also won't take much time and will very much help you determine whether this is a beneficial tactic for your company.
One word of caution: Do not allow yourself to be sold on the idea of using an automated commenting software or even outsourcing this to anyone who is not a recognized spokesperson for your company. A key aspect of this strategy is developing relationships with respected bloggers who have access and credibility with your ideal audience. It's about relationship and it doesn't take many solid connections with audience gatekeepers to have a very significant impact on your bottom line!