My top 6 healthy seeds

Like any other food, seeds are best when eaten in their raw natural form. In terms of nutrition - any kind of heating or roasting reduces/destroys the nutrients. Any oil will be vastly different in terms of its nutrient content than the food from which it was derived. That is because the oil is only an isolated portion of the whole food. For example, sesame oil does contain the fatty acids found in sesame seeds as well as the vitamin E and phytosterols but it doesn't contain any of the other vitamins, minerals, lignans,or amino acids that sesame seeds contain. Its not to say you cannot or should not use these oils but don't think you can replace your seeds intake by substituting them with their respective oils.

As a general rule, I do not take more than 3tbsp of seeds per day. 
You can Read about Seed Cycling and how you can use seeds to balance your hormones here. I try to follow this pretty religiously

1. Hemp Seeds:
Hemp seeds are truly a super food, as they are packed with an impressive list of nutritional attributes. Perfectly balanced with a 3:1 omega-6 to omega-3 oil ratio, they are also an excellent source of gamma linoleic and acid (GLA). Containing 10 essential amino acids, hemp seeds are composed of over 30% percent pure protein, making them an excellent daily protein source especially in a vegetarian diet. They are also composed of 40 percent fiber, the highest amount of any grain on earth.
Hulled v/s Whole Seeds: The hulled seeds - with the outer shell removed ( also called hemp hearts, shelled hemp) taste milder and pack more nutrients; the whole seeds give you more crunch and fiber. The hulled seeds need to be refrigerated and ideally should be added to cold foods
Hemp and marijuana are legally the same plant, but only one will get you high. The big difference is the level of THC in the plant, ie. the component of the cannabis plant that makes you high. Hemp has about 0.3%, marijuana has - 3%-15%

2. Sunflower Seeds:

The perfect phytochemical-rich seed for those of us looking to lose weight, as they promote healthy digestion and increase fiber intake. Sunflower seeds are also extremely rich in folate, a very important nutrient for women. They are packed full of good fats, antioxidant-rich Vitamin E , selenium and copper, all crucial elements in supporting heart health and balancing troublesome cellular damage.

3. Sesame seeds:

Sesame seeds are very high in calcium, magnesium ( helps lower Blood pressure), zinc (an essential mineral for producing collagen and giving skin more elasticity. zinc has also been shown to boost bone mineral density and bone health as a whole.) fiber, iron, B1 and phosphorus. Possessing important cholesterol-fighting fibers known as lignans, studies show that these seeds can lower blood pressure, as well as protect the liver from damage. Sesame seeds also may help prevent many health problems, including PMS

Black v/s White Sesame Seeds: The nutritional values of Black and white sesame seeds are very similar although Black sesame seeds contain 60% more calcium than hulled white sesame seeds. (1 tbsp of whole sesame seeds (52 calories) contain 9% of daily recommendation of calcium.) I personally keep both whole black and white sesame seeds and use them alternatively on salads, fruit mixes and smoothies. 

4. Pumpkin Seeds:

Pumpkin seeds are high in a form of antioxidant known as carotenoids, a special plant derivative that enhances immune activity and disease fighting capacities. These seeds are also high in are one of the best sources of plant-based omega-3s (alpha-linolenic acid or ALA) and zinc -  which is important for prostate health (where it is found in the highest concentrations in the body). Finally, pumpkin seed are high in phytosterols, plant components that aid in keeping stable levels of cholesterol and enhanced immune response. In order to preserve the healthy fats present in the seeds, pumpkin seeds should be eaten raw.

5. Chia seeds: 

Chia seeds are known for their abundance of Omega-3 fatty acids, making them a great alternative from fish oil for vegans. These amazing little seeds are an excellent source of high-quality fats, as they are made up of a whopping 34% pure omega-3 oils. The omega fatty acids can improve your heart health and cholesterol levels, and can be helpful in losing weight. These seeds contain an abundance of antioxidants, as well as complete protein, a rarity in plant sources. They balance your blood sugar and give you steady energy that lasts for hours . Chia seeds are also a great source of fibre. You can easily store them at room temperature for months. It is tasteless and doesn’t need to be grinded like flax, 

I sprinkle these seeds on just about anything from salads, fruits, smoothies to yogurt. You can even eat them after soaking in water for 10 mins - the gel that is formed around the seed with the help of water has no calories and makes you feel more full. Because of their mild flavor and are incredible capacity  of binding liquids - they are great as egg replacers in baking recipes

Most nuts and seeds have anti-nutrients like phytic acid that can make all the previously discussed important nutrients less bioavailable when you consume them. So if you plan on consuming seeds or nuts on a regular basis, it would be wise to soak or sprout them

6. Flax Seeds: 

• Flaxseeds are the #1 dietary source of a compound called lignans and the #9 source of polyphenols
• Lignans act as 1) phytoestrogens which help regulate estrogen levels in our bodies (important for hormone-related cancers such as breast and prostate), and are 2) beneficial fiber-like compounds which are important for digestive health (promotes motility and regularity) and immunity (the healthy bacteria in our colons use fibers for fuel – and these healthy bacteria are a part of our immune system)
• Lignans contain polyphenols which are antioxidants (also found in olive oil and berries) that protect our cells from damage and make our vascular system work more efficiently; polyphenols also support the liver byenhancing Phase 2 of the detoxification process
• Flaxseeds are also a rich source of the omega-3 fatty acid ALA and soluble fiber (important to cardiovascular health by decreasing LDL levels)

Flax is a pretty delicate seed that needs to be stored in an airtight container at cooler temperatures. It must be used in powdered form for the body to be able to digest it and extract the nutrients out of it. Ground flax seeds get rancid pretty quickly so either grind them at home in small batches (I do this) or store them in the fridge.
Find more details on Flax Seeds here

Ways to incorporate Seeds into your diet: 

• The most common and easiest way to eat more seeds is to add them to fruits, salads and smoothies. 
• You could also add almost all of the seeds to your to your morning cereal, oats etc. 
• Hemp can be easily added to pastas and stir fries (once they have cooled down a bit) and is a great way to get your kids to eat them. 
• Making seed crackers (heating would reduce their nutritional value but that's they are still going to be healthier than the store bought version) and using them in non-baked desserts is another great way to get some seeds into your diet. 

SOURCE: 1, 2