The following list is what I take from a supplement perspective and what I take reflects what I think is actually worth taking. Take my recommendations and reasoning into account when you're deciding what supplements are worth your time and money.
Fish Oil Fish oil contains DHA and EPA omega 3 fatty acids which are anti-inflammatory. If inflammation = disease, than something that is anti-inflammatory is a good thing for your health. Many processed foods, nuts, seeds and grains are high in omega 6 fatty acids, if you're eating a Standard American Diet (SAD) - note the irony in the acronym - you probably have a very high ratio of Omega 6's to Omega 3's. In order to manage inflammation and promote health and longevity you want your ratio to be as close to 1:1 as possible. To achieve this you can reduce the amount of Omega 6's that you consume and take supplemental fish oil to help you reach that 1:1 balance. One thing to keep in mind, for those that eat fairly clean, is that you also need to account for what your protein sources eat when you're thinking about what your 3:6 ratio looks like. If you eat pastured/grass fed meats, eggs and butter, wild caught fish, and limit your nuts and seeds you may not need to supplement with fish oil at all. However, most people probably eat some conventionally raised meats and eggs along with nuts and seeds, so keeping fish oil in your repertoire is a good idea if you're that person. So how much fish oil should you be taking? Now that is a tricky question...I go by the Robb Wolf Fish Oil Calculator hosted by Whole 9 for dosing recommendations. I do increase my fish oil consumption after hard workouts or when I'm feeling really sore and run down. I might also skip my fish oil for the day if I eat omega-3 enriched eggs and grass-fed meats for a day. Try it out and see how you feel, and if you are getting blood work check your c-reactive protein and shoot for a value below 1 to see where your overall level of systemic inflammation is. Note if this is high fish oil may help reduce it, but it could be high for other reasons, like hidden gut irritation, high stress, bad sleep, etc. When you are buying fish oil look at what's in it, many less expensive varieties have a lot of filler in those giant pills. Take a look at the EPA and DHA values listed on the back and use the calculator. Right now I actually take the Nordic Naturals Lemon flavored liquid Omega 3 version - and remember you want only Omega 3 - not Omega 6's! Flax is also another place you may find omega fats, but there is some science behind the way your body has to break down the ALA's that are found in flax seed that shows that its inefficient to try to get your omega 3's from flax. Just get over your fear of the large pills or try the liquid out - I promise its really not as bad as you think if its flavored it tastes mostly like lemon.
Vitamin DI read in a NY Times article that Vitamin D is the "it" supplement of 2010 and I agree that there should be an increased focus on your Vitamin D consumption. Your body has the ability to create Vitamin D from sunlight, but in our now sun-phobic society that is terrified of skin cancer many of us are blocking our bodies ability to turn UVB rays from sunlight into Vitamin D. Vitamin D isn't commonly found in most foods (primary food source is in fish like herring, mackerel, catfish, salmon...) which is why its added to some foods like milk. When you cut dairy out, you need to make sure that you're getting vitamin D from somewhere since clothes and sunscreen block our bodies ability to make it from the sun. Another way to take a Vitamin D3 supplement, I take between 1,000 and 2,000 IUs per day based on how much I'm outside that day. In my last blood test, even taking some Vitamin D and being conscious about getting some sun exposure without sunscreen, my Vitamin D levels were just barely above the recommended lower threshold. Vitamin D is vital to your health and is something that is difficult to get from food - unless you eat herring everyday - so should be something that you consider supplementing with. It's commented that the current RDA for Vitamin D, even through just updated (and increased) is still very low compared to the amount that is most likely needed for optimal health. Adding the Vitamin D test to your next set of blood work is inexpensive and worth it to help monitor where you are and how much you should be taking. This is especially important on the east coast as we're entering the cloudy winter season, I'm planning on upping my Vitamin D dosage another 1,000 IUs for the winter months - this should also help keep any seasonal depression at bay.
Magnesium I recently started taking a magnesium supplement around bedtime, specifically Natural Calm (pictured). You're probably thinking, magnesium I've never heard of anyone taking magnesium before, why do you need magnesium and what does that do for you? Magnesium is a mild muscle relaxant and also works in tandem in your body with calcium and it is important to have a balance of both for strong healthy bones. Along with calcium, magnesium also helps to prevent osteoporosis by allowing your body to absorb the calcium you take in through dietary sources, as well as supporting your immune system and muscles. I take magnesium - specifically the fizzy kind as recommended by Robb Wolf - and have noticed that it has dramatically increased the quality of my sleep. Another quality of Magnesium is that it helps reduce stress and helps me feel more rested when I wake up in the morning. Personally it doesn't make me drowsy, but allows me to relax and calm down - as a go-go-go Type A person this is a big deal.
Magnesium, like Vitamin D, is not found in notable amounts in many food sources, which makes supplemention worth considering. The magnesium supplement is a little costly compared to Vitamin D, but worth experimenting with, especially if you're a person that doesn't have great sleep quality. It could also help ease adrenal fatigue by helping you slow down and maybe even improve restless leg syndrome for anyone that has that need to move constantly even when you're supposed to be sleeping!
There you have it 3 supplements that I think are worth taking and you thought this was going to be a long list. When you're eating clean you get more than enough vitamins and minerals through your food so supplementing becomes just that, assistance in areas where real foods fall short. That being said, regardless of what you decide to take from a supplement perspective, your body is most able to use vitamins and minerals directly from the source - from food and sunlight - verses in pill form. So as much as possible shoot for eating a wide variety of colors in your vegetables, good quality patured meats and eggs, and shoot for 20 minutes of sunlight a day and you should be covered for your body's nutritional needs.