1. The Theme
First, decide on a basic "Theme" for your deck. This step is fairly cliche, since everyone suggests it. The advantage is obvious; just tossing in all the cards that look appealing will result in an unfocused deck that rarely works the way you want it to. So... how do you go about picking your theme? This is a problem for the creativity-challenged among us (like me at times...). Naturally, since I have no way of knowing what cards you have to work with, I can't pick one out for you. Here are some tips:
Using a well-known theme. There are many types of identified 'standard' or common themes that have been published in books and on the 'net. Here's a few:
Permission Deck - Make your opponent ask for 'permission' before playing any cards. This deck's philosophy is that your opponent can't win if s/he can't get his/her spells out. Typically blue, uses lots of counterspells.
Burn Deck - Beat your opponent senseless with direct-damage spells (like Lightning Bolt, Fireball..) and the odd cheap creature. Typically red.
Protection Deck - Use wards, circles and defensive magic to survive long enough to bring out powerful direct-damage spells or creatures. Typically white, but occasionally blue. Lots of CoPs, Wards and annoying spells like Gaseous Form.
Weenie Deck - Clobber your opponent early in the game with lots of cheap creatures. Occasionally tosses in one or two nasty creatures in case the game lasts long enough to need them. Low on mana, big on creatures. Almost any color can be used to make a weenie deck, from the most to least common (IMHO), white, red, green, black, blue.
Denial Deck - Prevent your opponent from being able to use his/her cards. Closely related to a Permission deck. Some decks force the opponent to discard cards frequently. Others try to deny your opponent the use of land (through Blight, Stone Rain, etc..) Others zap existing enchantments and fry creatures in play. Obviously, this can't win on it's own, and is usually helped along with some cheap creatures.
Discard Deck - Try to win by forcing your opponent to run out of cards first. Millstone comes in handy, any effect that forces your opponent to draw cards is also useful. This is an unusual and rare deck, since the cards that help you do this are few and hard to find.
Poison Deck - Give your opponent 10 poison counters. There aren't that many cards that can do this, so you'll need weenies and other defenses to be able to last long enough to win this way. This is also a rare deck, since it's hard to find enough of the poison cards.
These themes are great for beginners and experts alike. Keep your deck focused, and toss out the cards that don't "fit" with the theme, no matter how spiffy they may be.
Alternatively, you can use a 'networking' method to invent your own theme with your cards. Browse through your deck, keeping an eye out for cards that you think might be able to win the game for you if you could get them out. For the moment, ignore any glaring disadvantages you see about them like high mana cost or upkeep requirements. Set these cards aside. Once you've sorted through your decks, look at the ultra-powerful cards you've found. Are there any that share the same disadvantage? If there are, put the rest away and work with the few that have a common problem.
Now go through your cards again, keeping an eye out for cards that could alleviate the disadvantage. Does that nasty creature have a high casting cost? Bring on the dark rituals, Llanowar elves, Wild Growths, Mana Flares and any card that 'supports' your big card's disadvantage. In our example, say I went through my deck and pulled out the "Lord of the Pit". Nasty, 7/7 creature with trample. The problems, as I see them, are:
LotP has a semi-high casting cost. LotP requires a sacrifice of one creature every turn or it damages me instead.
These wouldn't be a problem if I had tons of mana and an huge supply of creatures... So, for support, I'll toss in
Dark Rituals provide instant mana. Breeding Pit, Serpent Generator and The Hive all generate creatures on demand. Raise Dead and Animate Dead bring creatures back to be sacrificed again Nether Shadows are cheap, and come back from the dead
You'll need to evaluate your creature's/spell's weakness yourself of course. LandHome is fairly annoying, but Phantasmal Terrain, Evil Presence, and Magical Hack can all alleviate the problem. The same cards can help out with LandWalk to make your creature unstoppable.
Once you've brought out all the 'support' cards, take a look at them and go through your cards *again* with an eye out for what else they might be used for. Why support one or two cards, when you can support half-a-dozen? Going back to our example with a Lord of the Pit, I notice that as long as I have lots of manufactured creatures, animated dead and cheap creatures... I can use them to fuel Ashnod's Altar for lots of mana, Fling them at the enemy with the Mogg Cannon, Stone Giant or Skull Catapult, sacrifice them to the Fallen Angel and a range of other devious uses. Putting other cards that can also be supported by the same "support" cards in your deck helps ensure that you won't be sitting around waiting for your One Killer Card to show up.
It's called the 'networking' method because once you've picked a card, supported it's weaknesses and brought in more cards that can be supported by the cards that support the first card's weaknesses, you repeat the process... Re-evaluate the new cards you've just brought in, look for common weaknesses again, bring in more support, bring in more cards for the support to support. Starting from just one or two cards, your deck can grow past the 40-card or 60-card minimum in no time.
This chart may seem confusing; It shows the average length of time (in turns) it will take you to get all the mana you need from basic land sources. For example, in a 2 color deck (say Black/Green) it will take an average of 15 turns until you have 3 swamp AND 3 forests. If you needed 3 green mana to cast one particular card, you'd have to wait 14 turns to get it. You might get one type of land earlier, but it's just as likely to be the one least useful to you as it is to be the type you can use. The chart shows about when you can expect to be able to cast that 3 colorless + 3 black Lord of the Pit card in a multi-colored deck.
You can see from the chart that if you put LotP in a 5-color deck, you'd be waiting until turn 44 to finally be able to cast it. In fact, in a 5-color deck, you might be waiting to turn 19 to cast even the weakest 1 colored + 1 colorless spells!
This makes artifacts (which don't care what color mana you use) and 'Mana converters' that can turn one kind of mana into another especially important in a multi-color deck. However, they are also taking up space that could be used by nastier creatures and more potent spells.
This leads to the following guidelines for creating a multi-colored deck; 2-colored deck: Have very few cards that require 3 or more of one particular color. 3-colored deck: Have very few cards that require 2 or more of one particular color. 4-colored deck: Use artifacts and artifact creatures as much as possible. Consider using a few mana converters; some creatures can turn one color of mana into another. Several artifacts can do the same. 5-colored deck: You almost definitely need mana converters or dual-colored lands. You will almost certainly need cheap artifact creatures to defend yourself with until you can get your spells out.
In general it's best to stick to 3 or fewer colors. If you want to use more than two colors, it's usually best to have only a few spells of the 'odd' colors and either only a few mana sources, or none at all for them (rely entirely on converters like Mana prism).
5. Trimming
New players often have difficulty keeping their decks down to a small size. If you go too much further over 60 cards (or 40 if that's the minimum size) you'll need to trim your deck a bit. You certainly don't need to have an exactly-60 card deck, if you go a few cards over that's nothing to really worry about, but 10 or more cards is pushing it.
With that in mind, here's some tips on how to trim your deck down to size.
Consider the versatility of each card and how often it will be useful. A CoP: Black is useless if your opponent has no Black offensive cards. It is less versatile than Fireball, which can target either creatures or players and does a varying amount of damage.
Generally toss out color-specific cards unless you have some way of making them useful in the event that your opponent doesn't have the color they work against. A CoP: Green becomes much more useful if you have the leprechaun that turns creatures that block it into Green cards...
Toss out cards that require your opponent to have something specific to be useful. A lot of blue creatures have Islandhome, which is useless if your opponent doesn't have islands.
Flying creatures are more versatile than non-flying creatures with the same abilities (usually; a notable exception is the Thicket Basilisk vs. the Cocatrice)
Toss out some of the 3rd/4th level support cards.