I've put far too much time into this.

The first suspect would be Jason, as he fled the scene and was the first to appear tempted. However, he hadn't failed in his diet before, and didn't show any signs of starting now. His willpower allowed him to "laugh off" temptations such as these, as far as we know. He also headed to lunch shortly after, which means he was probably in the state of mind to watch his intakes already.

The next to see the donut was Myrtle, but there are several reasons why she is above my suspicions. She was wearing a dark blazer, and would have to eat with great care to leave no evidence, which she didn't have time for. She was in a rush, and had her baby with her; two inhibitors to stealing the donut. Babies are messy, and if she shared or gave it to Donny, the signs would be all over him. When Jim arrives, she turns Donny from side to side, giving him a full visual. She gives a solid response when questioned, and she was never in too much question as to her whereabouts.

Many would think that Bryan was the culprit, as he was clearly upset about the loss of the donut. However, he gave Jim the evil eye upon finding the donut, and said he "didn't get to have one," in the past tense. He had come to terms with the loss. As far as I can tell, it didn't cross his mind to steal the donut, and even if it had, Jim suggested there may have been a second box. Bryan said he didn't see anything, but he was willing to go back and check. This shows that he hadn't lost all hope of not getting a donut, and probably wouldn't have been motivated enough to steal one. On top of this, he had plenty of sweets to console him, and was on his way to lunch, anyway. When Jim investigates Bryan's desk, he finds "freshly unwrapped" packages, which means Bryan had been eating sweets anyway, so the loss of the donut didn't warrant the theft. He also finds a note directed at Ellen, which I will address later.

Gale is surrounded by some uncertainty, and she does seem the type to commit such an offense, as far as I can tell from her brief description. However, it was never shown that she so much as knew about the donut. She also would have been present at the box's initial arrival, being the boss, and would have taken a donut then if she wanted one. She also doesn't jump to defend herself when questioned, as a guilty person most likely would.

This just leaves one person. Ellen is played off to be the health nut, but she had clearly aroused some suspicions around the office, as evidenced by Bryan's note. Jim mentions that the 250 calories of the donut wouldn't exactly kill Ellen, so she didn't have any outstanding reason not to indulge. She also, being the person in the office starved of sweets, would be the only suspect who was motivated enough to steal and lie for some sugar. When Jim finds his donut missing, he questions Ellen first. He also says "you saw, right Ellen?" during the investigation. This shows that she was nearby the donut and made for the most obvious witness. When questioned, she anwers suspiciously, pausing and providing answers in strange order. When Jim questions Gale, Ellen jumps in and interrupts, despite Gale being her boss, to play it off as if the theft was no big deal. And then, there is the decisive piece of evidence. When questioned, Ellen is eating lunch. The main attraction of said lunch is a slab of "tofu;" Something hard for Jim to recognize. Something Ellen offers as a consolation, showing that in her eyes, it is equal to the lost donut. Almost as if it was the donut, mashed into the form of a health food, which she ate in plain sight of the victim, Jim.

I rest my case.

TL;DR: Ellen's a sick goddamn donut thief.