Basically, you pick a profitable niche for your online business, and then you find an affiliate partner who has products available in that niche. Some of the most popular affiliate sites are Clickbank.com, Amazon.com, and CJ Affiliate by Conversant (formerly Commission Junction). Between them, they offer just about any digital information product (like ebooks, audio files, video files) or physical product you can think of. May big name companies and brands, like Wal-Mart, Home Depot, etc. run their affiliate programs through these third-party affiliate sites.
In the long-term, it affects your versatility, functionality, and, of course, your brand. In the short term, it can certainly add/take away a lot of headaches. That said, just like choosing a physical house or office, there is no such thing as an absolute “best” or “top” choice. There’s only the right choice relative to your goals, experience, and circumstances.