These are my 5 tips to putting together the best possible overall portfolio-
1. To put it simply, edit down your images! Portfolios ideally consist of 20-40 cohesive images that flow together, demonstrate your style and show range (if you're good at multiple niches you may want to consider creating multiple portfolios). To do so, often times you need to edit out thousands of images. I accomplish this by either recalling successful photo shoots to look through, or by quickly browsing through the large picture thumbnails of my library. A good rule of thumb for editing your images is looking from a customer's point of view. Think of your audience! Is your "worst" image in your portfolio still good enough to encourage potential clients who don't see anything else? Remember, a portfolio is only as good as its weakest link.
2. Look for unique and visually compelling photographs for your portfolio. Remember to not only show amazing shots, but ones that are hard to take and shows range.
3. When creating any type of portfolio, presentation is important. If the portfolio is intended for online use, I recommend having a clean background that doesn't detract from your shots. When creating a physical copy of your portfolio I suggest printing large copies of your work on glossy paper and using acid-free plastic sheets as covers. Your physical portfolio should be able to be adjusted and transported around. Remember outside presentation is also significant, so it may be worth it to invest in a cool case for your images as well.
4. Both online and physical portfolios should show-off accolades and publishing of your work.
5. When creating portfolios for clients, know what they want ahead of time: stylistically, artistically, or topically. If they haven't provided anything specific just bring your best work. For more on the client process, read a past post: http://bit.ly/fiLmkv
My suggestion for making online galleries of your work is SmugMug and Wix.