Thanks as always to everyone that assisted in the comments.
Click on the images to see larger versions
Puzzle 41 - Cutting Corners
Puzzle 42 - One-Eyed Royal
Simply follow the line of the eyes of the three cards and use the corresponding letters.
The clue of course being, "it's all in the eyes"
Puzzle 43 - Picture This
Arrange the pictures so the blocks line up.
Then take each column of blocks and rearrange into the column number order and read the answer.
Puzzle 44 - Want ads
The puzzle clue is "Substitute", you need to swap some letters around -
O = D
D = O
U = E
E = U
P = A
A = P
Y = T
T = Y
Puzzle 45 - Solitary Man
A very clever way to finish the set of puzzles and it had us guessing all day.
The answer was obtained by waiting for the times scratched into the wall, and as Alcatraz is in San Francisco it was Pacific time of course.
The shadow of the window bars lined up with a letter at the specified time to spell the very appropriate final word.
The image used above to circle the letters was originally posted in the comments by LeeL.
I'm in the UK and didn't stay up to see where the cross landed at those times, but it is the correct answer.
The second image is a composite of all the actual times created from pictures sent in by ObFuSc8
A fun way to solve this as you follow the directions in the car chase in the Final episode of Alcatraz Season 1