I am finding jobs through job boards and if the company has a website, applying directly through there. Are there any advantages to doing so as compared with applying from a board such as Dice, Monster, Careerbuilder, etc? Does it look any less/ more professional to bypass the middle man (the job board in this case) and apply directly on their site?
Some companies use job boards rather than their own websites, that's the only one I can think of. Even the ones that use job boards have a link on their website.
Personally, I would go to the company's website regardless, as you can do a little legal corporate espionage to learn about the company, their values, culture and interests (then over to the financial sites to see how stable they are)
As to if it looks more professional...
If I were a hiring manager and knew that you came to our site to look at our company, you'd move to the top of the list because it tells me that you're not looking for "a" job, but that you are interested in my company. I'd consider that far more professional than digging through the job sites and applying to anything you think you're a good fit for that position.
It tells me that you want to work for my company, which is going to get my interest.
The reasons companies post their open positions on more than just their own website is that they increase their chances of reaching potential employees.
Do I look like I'll be happy to go through 50 different websites for 50 positions? That would be quite a time suck. Never mind that I'll be missing some pretty big websites such as google.com. Yes, I could make a persistent hot link to google.com and make quite a career out of looking for a job with Google but I'd be doing it at the opportunity cost of every other company I want to contact.
It's more efficient for me to go to a one-stop website such as dice.com or linkedin.com and go for just the positions I want. Of course, Google and others are aware of what I and others are doing and why we are doing it, which is why they have open positions on that one-stop websites.
You're complete failure as an angler if you idea of fishing is you telling the fish to come to you. I go where the fishes are and I make sure that I have at least one fishing rod set up for each spot where I think the fishes are. Google is not fishing for recruits any differently than I fish for fish.
There is or should not be any difference between you going directly to a company's website for open positions and going to a one-stop website. The reality depends on how much enthusiasm HR has for updating the company's open positions on the company's website and at the one stop website.
Having said that, if you are getting an interview with the company, that company's website may be your primary source for research on the company, which the Google search engine running a close second. If the company were indicted for example, its disclosures on its website about its days in court might be very limited.