Playing Ib again in a few years made me realize that there were so many things that stood out to me as blatant foreshadowing. Without saying anything more, let's start.
There will be spoilers! Everything is ordered in their order of appearance throughout the game.
Ib is told to keep her handkerchief in her pocket. In all but one route, this handkerchief is never used. In the route of Promise of Reunion, Garry's finger is cut from the glass breaking when they burnt Mary's portrait and the option of giving the handkerchief is shown. This then causes Garry to remember Ib once they go back to the Guertena exhibition.
Main Gallery Display
This part assumes that if you go upstairs first.
Garry could be seen standing and looking at the Hanged Man as soon as you head upstairs. Garry becomes a traveling companion and playable character, whilst the painting itself is a reference for both Garry and for one of the areas later (as an ending replaces The Hanged Man with Forgotten Portrait, and The Hanged Man is used for a puzzle).
Resting on the Reserved Seat
Reserved Seat is found on the second floor and in the gray area, the room in which Ib and Garry gets stuck in and ambushed in. (And, apparently, according to Garry, there is no time to be sitting around.)
The Enemy, Lady in Red & Death of the Individual
The infamous Lady in Red is shown to be a reoccurring enemy in the game and can be seen in the upstairs area of the museum. Death of the Individual also appears as an enemy on the same floor as Lady in Red.
The painting is where Ib spends a majority of the game. Let's not forget that Lady in Red, a rose, and each color of each area is there (which is blue, green, brown[?], yellow, pink, black, purple, gray, red).
The Puzzles & Abyss of the Deep
Perhaps the most obvious example of foreshadowing is Abyss of the Deep, when one of the puzzles asked for the large painting's name.
If you explore so much, you find the rose that ends up to be the representation of their spirit. The roses that each playable character finds ends up as their life force (except for Mary, which is a fake rose).
Early on in the game, Garry gives Ib a piece of lemon-flavored candy when Ib wakes up from collapsing. When the white ant in the dungeon asks for something sweet to eat, Ib has the option to give the candy to it. In Together, Forever, Mary eats the candy if it is still in Ib's inventory. In the route to Forgotten Portrait, Ib would have to eat the candy to make space in her inventory to take Garry's lighter .
Ib & Garry come across a painting of Ib's parents, dubbed Couple. Later on, if you have gotten as far as to go to either Memory's Crannies or Promise of Reunion, Ib's mother comes from the portrait to attempt to get her back.
Separation and the Actual Seperation, and Books about Separation Seperation is the painting that both Ib and Garry looks at before the room blacks out entirely, causing Garry to use his lighter. This represents Garry and Ib being separated from each other, which happens when Flowers of Jealousy separates them. Garry can also read books about separation and the factors of either being together and being alone (in the Tree/library room and in the room in which Red Eyes are in).
Garry's lighter would eventually be a very helpful asset in Ib's journey, first used when the lights go out in the room with the painting dubbed Separation. It would be used as light, burning down things, etc.
Upon meeting Mary, Garry tells Mary and Ib to not trust their roses with others. Later on in the Sketchbook, if it ever comes to the point that Ib's rose is in danger of being plucked to the brim by Mary, he would eventually have to betray what he had told Mary and Ib.
Garry's Rose & Mary's Obsession with Blue
When Mary literally bumps into Garry and Ib, she states openly how she likes red, but blue even more. This is made more apparently obvious when, if running into Forgotten Portrait or Together, Forever, when she states that she likes Garry's rose better because of its color.
Isn't it cute?
Entering the room with multiple rabbits (or horrifying dolls, in Garry and Mary's case), Mary asks Ib if it's cute/pettable/or if she's unsure about the entire thing. If Ib's rose is given to Mary in the Toy Box, Mary may bring up the point that Ib had said it's cute (if Ib agrees with Mary).
Mary & Her Palette Knife
Mary uncovers a palette knife in one of the boxes, which eventually is used in most routes.
Mary's Homicidal Tendencies
Mary displays this clearly. Mary stabs a mannequin, which is in her way, and laughs quite a bit (much like that blue...thing in the Gray Area). This is then used against Ib and Garry when she is hunting them down and especially when she is chasing Ib (and Garry, if he is still alive) in her "room".
Mary & Playing Doll House
When talking with Mary after stabbing the mannequin, she mentions about playing house and Ib being one of the relative dolls, presumably a relative doll to Mary, which is true in the Together, Forever ending.