Clark's biological father, Jor-El, made his will known to Clark and his adoptive parents, the Kents, on several occasions through the use of fiery symbols. The first example of this was in "Rosetta;" Jor-El caused Clark's heat vision to go haywire and burn the "hope" symbol on the Kents' barn.

Seeing coverage of this weird event in the newspaper is what prompted scientist Dr. Virgil Swann to contact Clark.
When Clark refused to obey Jor-El and leave on a mysterious journey for him, Jor-El burned the El family crest onto his extremely muscular chest. The conversations father and son had in "Exodus" is as follows:
Jor-El: |
Fear not, Kal-El. |
Clark: |
Who are you? |
Jor-El: |
I am Jor-El... Your father. |
Clark: |
I thought you died! |
Jor-El: |
I am his memory, his will. I am to fulfill his promise and guide you all the days of your life. You are the Last Son of Krypton. When you traveled through the cosmos, you carried the hopes and dreams of your people. They now live through you, Kal-El. It is time. |
Clark: |
Time for what? |
Jor-El: |
Time for you to accept your destiny. |
Clark: |
I don't know what you have in mind for me, but I-- |
Jor-El: |
By the setting of the sun Sol, you will return to me. Your destiny will be fulfilled. Your thoughts are not a mystery to me, Kal-El. |
| [A vision of Martha, Jonathan, and Lana appears.] | |
Jor-El: |
But these people have served their purpose. It is time to leave them. |
Clark: |
Please! Everything and everyone I love is here in Smallville! |
Jor-El: |
You must let go of your past. I will guide you to your future. |
Clark: |
No! I don't want your guidance! I want to create my own future! |
Jor-El: |
You have no choice, Kal-El. |
|
[At sundown, Clark goes back to the cellar.] |
|
Jor-El: |
You will obey me, Kal-El. |
Clark: |
You're not my father. I won't let you control me! |
|
[A beam of light from the ship blasts Clark into the air, branding him.] |
Clark: |
NOOOOOO! |
Jor-El: |
This is the mark of your ancestors. You cannot fight it, Kal-El. At the zenith of the star Sol, you will begin your journey. If you do not, you will hurt the ones you love most. |
Below are three pictures of Clark's beautiful, albeit branded, torso. After he was branded (first picture), Clark ran off to Metropolis under the influence of a red kryptonite ring, and the brand reacted badly to the poisonous RedK. The second and third pictures show Clark's brand reacting to the presence of RedK.
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Side note: Yes, costume people, Tom Welling is VERY muscular, and I very much enjoy seeing those little ridgy muscles above his hipbones (wish I knew what those were called... I call them "I wish I could grab onto those!"). However, no straight man-- alien OR Earthling-- would wear his jeans so low. Or have what appears to be a Brazilian wax. This is part of what fuels the rampant Clex community, TPTB!
Jor-El kidnapped poor Clark at the end of Season 3 and whisked him off to a birthing chamber inside the walls of the Kawatche Caves. He burned a symbol into the Kents' cornfield to send a message about Clark's whereabouts. As Bridgette Crosby explained to Martha in the Season 5 premiere, the symbol means "crusade."

Clark was in the birthing chamber for three months (conveniently, just long enough for the summer break between Season 3 and Season 4!). Here's a nice shot of Clark inside the birthing chamber in a position that makes a familiar symbol ("Covenant") as well as another of him in the cornfield after he is beamed back to Kansas during his rebirth ("Arrival"):
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The El crest appeared in a somewhat transformed manner during "Relic," the flashback episode that explored a young, rebellious Jor-El's visit to Smallville in the early 1960s. The necklace "Joe" wore during his stay, which is actually a Kryptonian gadget that stores memories, like a diary, is shown below:

See this page for how the medallion is linked to the Kawatche Caves.
Finally, take a look at this cool shot from "Crusade" that shows Kal-El and Clark fighting for supremacy. The two halves were released thanks to Martha exposing Kal-El/Clark to black kryptonite (courtesy of Swann's assistant, Bridgette Crosby).

Looks a tad familiar, doesn't it?