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Harry doesn't know immediately why Tom doesn't register as normal to his first glance. Second glance. Third.
Tom has fairly symmetrical features - there are no anxious tics to occupy his hands, no abrasions to mar his pale-but-not-pasty complexion, and his height is fairly average to the rest of their year. He is an upstanding student and makes good marks, if the grapevine can be trusted, but he doesn't volunteer information or answers often enough in class for Harry to mark his aptitude one way or the other.
Harry doesn't quite know why he's so hung up on this one Slytherin, but it's become enough of A Thing that Hermione and Ron have begun to side-eye one another whenever the two occupy the same space. Unknown to an oblivious Harry, Tom has begun to catch on to Harry's constant scrutiny and returns it in kind during those off-moments when Harry finally focuses his attention elsewhere.
It's both a boon and not, Harry's aversion to eye contact - though he misses whatever Tom's immediate stare might communicate, piercing and placid as it most often defaults, he gets to see the Slytherin in moments where reading the indent at the corner of his mouth and the tilt of his head is most beneficial way of discerning his person.
Harry has gleaned a few things over the course of his analysis.
There's an almost military ease about Tom's posture and bearing when he is attentive in conversation, his hands finding their comfort loosely clasped about the wand held at his back. It's a natural parade-rest, though one sharpened infinitesimally by the implement constantly at hand. Harry was wrong about the fidgeting, too. He just hadn't noticed it before - there's a reverence about the way Tom handles his wand when he is conversing with his peers. His fingers likely know the grain better than his eyes, at this point, neatly-buffed nails and sedulous fingertips pattering and smoothing and ascertaining every groove and dip and end whenever his thoughts veer elsewhere.
(This wouldn't be so unusual if Tom didn't hide the ritual behind his back like a dirty little secret.)
There's something else, too, but it isn't until Harry decides to people-watch for a while in the common room during a chess game with Ron that an idea starts to gain some traction.
Ginny and Dean are laughing by the fire, the two of them sharing an armchair, and Ginny's smile is not all that different from Tom's - at least, not at its culmination. Their mouths both turn upwards at the corners, though Ginny's more is quick compared to Tom's steady deliberation, and their eyes both crinkle with that natural surge of breath that comes with latent merriment.
Conversation eventually moves on from whatever joke made Ginny laugh, perhaps to a topic more neutral. It's enough that Dean's face has shifted from its jovial grin to something more sharp and cutting, but Ginny's face is not quite there yet - there is a suggestion of that smile wrought by their previous topic, lingering traces of mirth found in her crinkled nose, her squinted eyes, and her curled mouth.
Traces. Smiles stay on the face even after a joke has come and gone, because while the mind might have moved on, the physical expression of joy, interest, sadness, hurt, or anger don't just get tucked back into an arsenal of conscious reactions and intentions…
… unless you're Tom Riddle.
Tom has a… really nice smile. Harry probably wouldn't say this to the boy's face, but there's something angelic about how it makes his whole face glow, his mien lilting into a crooked-grinning delight that jerks his head to one side, meticulously-parted fringe cutting across his forehead in an artful display of tousled imperfection.
But when the person at which it's directed looks away (and how they manage that, Harry doesn't really know), Tom's features gradually shutter, the vibrancy of before put away like so much clean laundry. His smile is pressed, his posture straightened, his ebullience folded. Where before this might have registered as a product of Tom's probable vast intellect - his thoughts running quickly enough that his face has learned to catch up - Harry now sees the deliberate nature of his dissemblance.
When Harry sees Tom next, he finds himself proven correct. And if his heart skips a beat or two at the slow, sharp, intent-ridden smile that accompanies dark eyes finally meeting green, then that's nobody's business but Harry's own.