When you do find small airlines, even if they are listed in a search engine results, it often pays to check the company site which may reveal exclusive online offers not found in a regular search engine. For example, when flying in Western Canada, I found that Hawk Air, a small and local company offers weekly deals on certain days. Be sure to double check!
Use skyscanner.net. This neat website searches all airlines, big and small, and allows you to look for the cheapest rates out of your local, rather than getting bogged down with specifics. Meaning, if you know you want to go on vacation but aren’t too picky about where, this website will provide the cheapest flights to everywhere in the world from the nearest airports to you.
In Google Chrome or Safari, incognito is enabled by hitting Command (or “Control” if using PC), Shift, “N”. For Mozilla Firefox or Internet Explorer, hit Command (or “Control” if using a PC), Shift, “P”. This will open a new browser window where your information is not tracked, thus not inflating prices as you search. Note: if you're using an older version of OS X, open Safari then click “Safari” in the menu bar, and select “Private Browsing”.