It seems that businesses on the net are reflecting more and more of what is going on in the regular world of brick and mortar stores. In the 'Offline' world we are seeing big box stores like Walmart, Costco and The Home Depot making it difficult for 'Mom and Pop' stores to survive. In the 'Online' world we are seeing something similar where big companies like Amazon and EBay have seemingly unlimited budgets and are targeting an endless number of keywords.
So will there still be room to compete with these giants? With a little bit of love and attention, smaller sites can stay in the race. While these big companies are off bidding on millions of keywords through various advertising platforms they may not have the time or product knowledge to target their ads properly towards individual keywords. As the owner of a smaller site you have the advantage of dealing with less keywords which can give you the time to accurately target your terms with specific ad copy and landing pages. Dealing with less keywords then the big companies also gives you the advantage of being able to test your ads more thoroughly so you are able to find the ones that covert the best.
Big brands are also going to make it more difficult for the little guy in organic search. Google seems to love large powerful websites so we will probably see these sites encompassing more of the market in the future. Just as in Pay Per Click, the advantage that a smaller website has is that it can be much more specific about how it targets keywords. To keep up, small sites won't be able to sit stagnant; they will have to be high quality and consist of great content. As a small website you will want to show value in the industry to gain natural quality links. Big companies will almost always get the quantity of links but as a small site you can target the quality.
Big companies are only going to become more prominent as time goes on, but that doesn't mean there isn't room for the little guy.