Mordekaiser is a really competitive pick for a top/mid solo in ranked solo queue. He can fit into team ranked 5's but because he lacks any form of CC without Rylai's Crystal Scepter and is extremely vulnerable to CC himself, there are better champions which fill his role.

Versatility - Mordekaiser can be built with a variety of defense and offensive AP items. AD items can work for him but it's only situational.

To summarize, Mordekaiser is a champion where offense is the best defense. Great solo who can win lanes without too much difficulty and snowball quite well.

STRENGTHS:
Tanky
DOT magic spells
Spammble short cd aoe nukes
Can turn teamfights with a well placed ultimate
Strong base damage

WEAKNESSES:
Spells cost health
Ignite/regen reduction
CC
Items do not scale that well into late game

WARNING - THIS WEBSITE HAS OUT OF DATE INFORMATION ON SPELLS. FOR EXAMPLE THE ACTUAL Siphon of Destruction has 0.6 AP scaling instead of 0.4.

The above setup which I highly recommend gives you exactly 700 HP (7 bars of health) with ~19 HP5.

For quintessences, viable options are-
S - Greater Quintessence of Health
S - Greater Quintessence of Vigor
A - Greater Quintessence of Movement Speed
B - Greater Quintessence of Magic Penetration
C - Greater Quintessence of Ability Power

Mordekaiser has sub-par starting health. If you are facing a strong laner and a ganking jungler, you weakest time is from LV 3-5. At LV 6 your ultimate can save you but since it has a rather long CD and is vulnerable to Ignite, greater health and health regen is extremely important. Once you die, your enemy top is fed and free to gank your other lanes.

Marks-
S - Greater Mark of Magic Penetration

Without doubt you buy these. Mordekaiser has good base damage but weak scaling (not bad but inefficient).

Seals-
S - Greater Seal of Vitality / Greater Seal of Health - Crosses at LV 5
S - Greater Seal of Vigor / Greater Seal of Regeneration - Crosses at LV 4
B - Greater Seal of Armor
The growth health and health regen runes are at 410 IP each while the flats are 820 IP each. The armor seals are 210 each.

Some people like the flat health/regen but in my experience you don't need that much regen from LV 1-3 anyway. Most of the health lost is from the cost of your spells rather than being harassed. Use your spells judicially so that you can last hit as well as generate a full shield. Not all champions are easily harassed by your Siphon of Destruction. Your priority is to farm well while maintaining health.

Flat health gives your about 48 health from start. Growth health runes in fact heal you about 10 HP as you level. So if you get ganked with flat runes you get (48 - 9.72 * LEVEL) more health to work with. Not as significant as you think.

Feel free to mix and match health and health regen runes (and growth and flat runes) to achieve your maximum effectiveness.

Glyphs-

A - Greater Glyph of Cooldown Reduction / Greater Glyph of Scaling Cooldown Reduction - crosses at LV 13
B - Greater Glyph of Ability Power / Greater Glyph of Scaling Ability Power - crosses at LV 6
B - Greater Glyph of Magic Resist / Greater Glyph of Scaling Magic Resist - crosses at LV 10
C - Greater Glyph of Magic Penetration

Assuming you buy 9 of each type of rune -
1. The flat CDR runes give about 6% damage increase in all spells throughout the game. (should you choose to spam them infinitely; assumption feasible in teamfights)
2. The growth CDR runes give a maximum of 9% increase in all spell damage.
3. Flat AP gives 9% damage increase with level 1 Siphon of Destruction; 4% increase with level 3 Siphon of Destruction; 2% increase with level 5 Siphon of Destruction.
4. Growth AP gives upward damage increase of 7.5% for level 5 Siphon of Destruction. 5.3% increase for Siphon of Destruction at level 13.
5. Magic penetration glyphs only give 4% damage increase for all spells and will scale down as your opponent's magic resist increases.

Both CDR and AP runes compete strongly for the glyph slots. Magic penetration is very weak and should not be considered. It is stronger when coupled with other magic penetrating/reducing mechanisms but only slightly. I personally choose CDR over AP because 1) when you get Rylai's Crystal Scepter, more CDR equates to more application of the slow and 2) AP does not scale as well on Mordekaiser's other abilities.

A standard 9/0/21. Mordekaiser needs as much CDR and magic penetration as possible. Adjust according if you take other summoner spells.

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