Schematic layout is nice and tidy, labeled.
Not clear to me what the Pi header needs; seems suspicious that there's a "INT" line with a whopping 0.1u on it. But the reset paired with it, does not; though following it down there's a whopping 1u (C3). I doubt this actually causes problems, but it may be counterindicated for best results -- the slow transition time allows the receiver (MCU input) to read an indeterminate value for a long period of time, making it more sensitive to noise or oscillation. (I think those pins have, or usually do, hysteresis (Schmitt trigger) so it shouldn't lead to oscillation, so that leaves sensitivity.)
Don't worry about doubling up cap sizes, just spread around a few larger values (1-10uF say, preferably with ESR to dampen the supply) and keep smaller local values (so, C9-C16). I would also be fine with sharing U1 pins 2, 44 between a single cap.
You do have C5 in there, so it might be an opportunity to drop the 1u's for fewer 10u's, give or take what impedances/time constants you need or can adjust.
What are R28-R30 doing? Forgot to assign some GPIOs..?
Sure got a lot of use out of that SMAJ15A. I wouldn't have a problem using a smaller (cheaper?) diode in some places. Can drop D10.
Hm, I'd put F1 on the other side of D9. Not a big deal.
The one thing I really wonder about is all the pulse filtering: the fan tach is just open collector, isn't it? So you won't get proportional PWM to voltage filtering, the source impedance is bouncing between ~470R (pulled down hard) and 5.57k (pulled up gently, uh in parallel with whatever might be in the fan itself too). The slopes are unequal and so the filtering will not be linear.
Better to just capture the PWM directly, using the timer and input capture. This might be a bit bothersome on a MEGA32, not sure. Fancier ones (XMEGA, MEGA0, DA etc.) do have more advanced peripherals that can count duty and period nearly automatically; YMMV.
Oh or uh, it's not really PWM since it's a tach, but the filter sets the maximum pulse rate that can be measured, which seems rather low with these values, and again, it's asymmetrical so it falls below threshold much sooner than you might've expected.
Likewise, PWM from MCU into C23, C28 isn't going to be happy. That's a lot of current through the pin driver.
Does the fan even need filtering anyway? Would it not be fine to just run logic level into it and let it deal with it?
You still want some EMI filtering but 1u's aren't necessary for that; maybe adding a 1-10n to the BOM would be worthwhile.
Also if you need a solid logic level so can't afford much filtering resistance, try a ferrite bead. A 330R (@100MHz) bead into 1-10n will do a good job for the most part. So, just an L filter, not Pi, should do.
Likewise on the RGB strips, those values are completely out of whack, 1u heavily loads the MCU and 8.2p does absolutely nothing. If those are the ~us pulses usually needed for that style of LED, I'd use a ferrite bead and a few hundred pF. Maybe an LCL (tee) filter with two ferrite beads, to give the MCU pin a somewhat higher load impedance plus add damping for the cable (so it doesn't resonate too much under ambient EMI).
Speaking of ambient EMI, for any connectors/cables, you can consider putting ferrite beads on them, whether on the cables themselves, or something equivalent in circuit. Note that individual beads per line, is not the same as one bead around the whole cable; to reproduce that on board, you need to use multi-line chokes, wired in parallel so they act together. For slow signals and power, it won't make a difference; for data signals it matters. (USB most of all, which has to be shielded -- make sure its grounds are tied into the circuit ground plane. That shield then covers the signals along their length, preserving logic levels.)
Finally, supply filtering, let's see: there's three 100u's on +12V? Probably fine. Make sure Q8-D11 is near one of them and that's fine. Actually that's the only active-switching thing on this side, could probably just cluster everything together around a 470uF or something. Just needs enough filtering to keep things not-too-bouncy between here and the 12V supply. Likewise for 5. C33, C37 seem rather overkill. If you need especially stable power for the MCU (not really, I don't see anything obviously analog needed here?) maybe consider running it at lower voltage (3.3 to 4.5V?) from an LDO, that way there's more voltage swing available on the 5V before disturbing it, and less capacitance is needed (even if the loads are strong).
Tim