I know every graduate students main concern with cooking "from scratch" and generally eating well must be the time it takes, followed by the cost. I thought it would take me too much time to prepare meals if I removed all processed foods from the grocery list, but to my surprise even when cooking more elaborate meals from scratch on the weekend it rarely takes me more than an hour from start of cooking, to meals eaten and dishes washed. Many days it's a lot less time because I incorporate left over side dishes (or main dishes) into the meal, which shortens prep time. And there are always lots of leftovers for tomorrows lunch box, eliminating all top ramen consumption.
Three investments that save lot of time and money, if you can afford them:
1. Crock pot.
How to use: add meat or veggies or beans, add seasonings and water, turn on and ignore for hours. Beans are the ultimate graduate student food. I know that amanda has mentioned it over at A Lady Scientist but it can always be said again. Beans are an excellent food source and can be purchased very cheaply from a number of places including in bulk at many grocery stores. You can't beat the crock pot for good bean soup (don't forget the split peas if you like that creamy stew texture.) Beyond the beans, start buying meat whole when possible (ie buy the whole chicken, not chicken breast one night and drumsticks 3 nights later) and toss all the bones and leftovers bits in the crock pot with a wedge of onion and few bay leaves and a few hours later you've go the start of a really great soup. A post doc in my lab told me you can also use your crock pot to make to-die-for hot breakfast cereal (start it before you go to bed, eat in morning). I tried this last week and it rocks!
2. Bread Maker.
How to use: Toss in all ingredients (maker usually has it's own specific order for adding these) hit the start button and ignore until the smell of fresh baked bread becomes distracting. A lot of people would argue that bread is so cheap that this is pointless. I disagree. I grew up strong and healthy on homemade bread and you really can't beat whole grain bread with no preservatives for taste and healthiness. Humans have survived on bread longer than any of us can remember, and it wasn't until modern food industry pumped it full of preservatives and removed all the healthy benefits of whole grain that we started thinking bread was bad for you. I just got a new bread maker to replace the used one I wore out (after 9 years!) and haven't calculated the cost of any of the new recipes I've been trying, but I did once calculate the cost for a rye loaf I used to make all the time. It cost $0.40 to make a large loaf of rye bread, 40 cents! and took me 2-3 mins to set up and toss the ingredients in. I don't know of any place you can buy good rye bread that cheap!
How to use: Keep as full as possible for energy savings. Avoid cheap to free ancient models advertised in the paper because your electric bills will sky rocket! We have a small chest freezer (5.3 cu ft.) and we keep it full year round. This is especially good for meat-eaters, and enables you to buy large quantities of meat from local farmers when it's in season, then enjoy for months to come. If you don't have any farmer friends you can buy from, go to the local farmers market and meet them. I can tell you that the meat you can buy at the local grocery is not the same in taste or healthiness. I would categorize a lot of meat for sale at our local chain grocery as processed food, which doesn't fit the food culture I'm adopting. But if you're of the vegetarian persuasion, fill it with the over abundance of summer harvest. Cooked squash can be scooped into a ziplock freezer bag and frozen flat, same goes for fresh summer salsa, steamed spinach, and a number of other items. And if you like to forage (like me) try the same trick with steamed nettles or field greens, acorns can also be frozen whole for later processing.