Stop saying "I have too much going on, and nothing will work."
Stop self-defeating is the probably the first step. Of course we have "too much going on," that's what we say when we lose control. Do realize that "too busy" can be a cause, but most of the time, "too busy" is more of a symptom.
Realizing that no one can drink up a whole river
Be it work, research, and teaching, they all work like a giant wheel or river that keep moving. No one can take the whole activity and "finish" it. Once I have realized that I am just moving things along from less to more refined shapes. It's noble to be a more responsible researcher/teacher, but the mindset has to be correctly set before burning one self out.
Use an urgency and importance matrix
Whenever I got a task I mentally assigned it into a quadrant of the the urgency vs. importance matrix. Then when I plan my weeks, I make sure to distribute 2/3 of available time to all the high impact activities. For the rest 1/3, I use it to deal with urgent and low-impact items or emerging items.
Avoid paper-based To-Do list
To-do list can be a confusing way to manage time because the whole process is high maintenance (keeping a list, some sub-lists, and constant correction and update) and frustrating (the list keeps growing, and yes, crossing out tasks feels great, but then you have a messy list.)
I just use EverNote to document my projects and tasks. When they are done, I move the whole index thread to "Archive." Index cards are a also a better alternative to a to-do list. When I am in a meeting or walking around, I put all strayed thoughts onto an inexpensive composition book.
As a side note, capturing strayed thoughts has a side effect on me as well. Most of the time, I kept mentally regurgitating works that I need to do and the long chain of tasks really bothered me. Once I spilled them out onto a piece of paper, then I stopped thinking about them for a while. When I have access to a computer, I change the thoughts into EverNote note page. This simple step empties up my mind to do some other more useful thinking.
Say no, say it a lot!
What about the urgent and low-impact? I just say no. This includes, but not limited to: grant proposal invitation sent to me when the grant is due in 5 days, meetings that really do not need me to be there (but I always attend the monthly staff meeting and faculty research meeting, just to be collegial), etc.
I used to suck at saying no, now I have a lot of elaborated ways to put it. And what's my elaborated way? Just say, "Thanks for the invitation/thinking of me. I am sorry that I can't help this round." And leave it like that.
One great trick for those who cannot say no is: you do not have to answer right there and right at that moment. Tell the people that you'll give it a good thought, and then say no afterwards.
Block your time in your calendar way ahead
Don't start filling in the calendar passively. Reserve your own time many weeks ahead. I fill them up with protected writing time slots. I write the best in the morning and love to do coding in the afternoon so I sprinkle all these little 30-, 60- or 90-minute slots across my calendar.
And I agree with @Nicholas' answer that this is a very useful technique. And this is not something that "sounds like the kind of thing that is nice in theory." I use this and Nicholas probably does too, and it really works. The harder you guard your time slots, the better it works.
No more, just three tasks a day
Leo Babauta's Zen to Done is an inspiring read and I'd recommend to people who think they have no time. I have adopted the idea of doing three Most Important Tasks per day. There are days that I barely got one done, there are days that I finished three by 1:00 pm and then spent the rest reading or learning new stuff.
Become a time freak
I time my tasks with a kitchen timer. I don't strictly follow pomodoro technique but I adopted the spirit of it. The way I operate is that I dedicated a chunk of time to a project, move it forward as much as I can, and when time's up, I consider my job for that project on that day is done. I do not binge work, because binge working is very prone to errors.
One very interesting side story. A colleague was chit chatting in my office and sudden the timer went off! The colleague jokingly asked me if her time is up. I explained to her my system. And oddly... since then whenever she visits me, she would add this question "Can I have __ minutes of your time?" before talking to me. Now everyone does that to me; and I do the same to everyone else.
Time to time, chaos and mess happen to us because we have developed an image of being easy going and flexible, two major magnets for chaotic and messy people. In fact, we don't have to. A good dose of rigidity gets you off a lot of ad hoc committees, "emergency" meetings, etc.
Identify what manifests the guilt
This is very important because the source of the guilt dictates how you resolve it. For me, the major source is fearing that I have upset the collaborators. I once dropped the ball on a secondary analysis and delayed it for half a year. Then this job gradually became low-impact/low-urgency. I decided instead of feeling awkward, I just went up to her after a meeting and apologize for not being able to finish the project. In fact, she didn't care as much as I expected; I felt a lot better having told her my thought.
Another fear is that people may think I am incompetent or chaotic. And for that, I have come to be very comfortable with myself. I resolved this issue simply for two facts: i) I am probably the person who cares the most what I look like in other people's mind. And ii) All other people are also busily caring how they look like in others' mind.
Practicing being mindful has many positive impacts on how I deal with these negative emotions. Now whenever I feel bad/good, I emotionally zoom out and look at the big picture, trace the connections, and examine the dynamics. I feel having this little slight detachment with emotion allows me to better tackle (either to avoid or to exploit) these emotions. Don't just feel guilty, ask why, why, why, why, and why. Yes, ask five times. Usually for me, three to four associations usually get me to the root cause, just like how they can get Toyota to their problems' cause.
I guess none of what I said is new. When it comes to time management there isn't really a silver bullet. From my experience, so far I have boiled down to only one truth: All time management techniques work if you use it regularly and seriously.