Sorry for the necro, but I feel the need to bump this because people are seriously underestimating the Doctor here. Sure, Doom beat the Beyonder, but tricking and defeating cosmic beings is practically the Doctor's bread and butter.
The cosmic hierarchy in Doctor Who is at least as complex and convoluted as Marvel's, but here is a brief overview:
Both the Time Lords and Time War-era Daleks have weapons/technology capable of destroying everything in the multiverse, save for themselves (the Final Sanction and the Reality Bomb). Furthermore, they were both able to pull out these technologies even when their resources were severely diminished (the Time Lords as they were losing the Time War and had been driven back to their homeworld, and the Daleks as just a small, recovering fleet that escaped the Time War).
Beings that are on this level or higher but don't generally need technology are known as Transcendental Beings, which are basically non-corporeal cosmic entities.
First of all, the Eternals. They are basically higher-dimensional, god-like beings (some of which embody concepts like Death, Time, Pain, etc.) Some of them were even worshipped as Gods by the Time Lords.
The Chronovores are Transcendental Beings that are possibly on the same tier as the Eternals, though generally weaker. Still, as their name implies, they eat time itself, and one Chronovore can easily devour an entire universe. Kronos, the strongest Chronovore, was the offspring of a Chronovore and an Eternal.
Also on the same tier (although still seemingly weaker than the Eternals) are the Great Old Ones, who are Transcendental Beings from the previous universe who survived the Big Crunch and Big Bang and were reborn into the current universe with immense powers (like Galactus). However, most of them are incapable of fully manifesting in this dimension, but they have powers to threaten the Time Lords and Daleks. Unlike the Eternals and Chronovores, who are both entire species with many individuals, there are only a dozen or so Great Old Ones.
During the height of the Time War, which was conducted on a multiversal scale, when the Time Lords and Daleks were going all-out and throwing everything they had at each other, the Eternals' reaction was pretty much "Wow, you kids are sure making a mess of our backyard. We're going to go somewhere quieter".
Above them all are the Guardians of Time, also known as the Sixfold God, 6 Transcendental Beings who rule over all time, space, universes, and dimensions, and are clearly abstract, embodying concepts like Chaos and Order on a beyond-multiversal scale. They are much more powerful than the Eternals and would often arbitrate disputes between them. There are only 6 Guardians, but just 1 of them is implied to be more powerful than the entire races of Eternals, Chronovores, and Great Old Ones combined.
Overseeing the Guardians of Time are the Grace, who basically appoint the Guardians to run the omniverse like TOAA appoints the Living Tribunal. On a similar level to them is the Glory, which controls and directs the omniverse.
Going by just the TV show, a quick laundry list of beings the Doctor has outsmarted/defeated include:
- The Animus, one of the Great Old Ones, also known as a Lloigor
- The Beast, who fit the description of a Great Old One, and was the psychic inspiration for every Satan/devil figure in the universe
- The Great Intelligence, another of the Great Old Ones, also known as Yog-Sothoth. Notable here is that the Doctor's own personal timeline was so complex and intertwined with the fate of reality that the Great Intelligence was only able to corrupt it as the cost of its own life, but the Doctor and his companion Clara fixed it.
- Fenric, another Great Old One, whose power was threatening the universe
- Sutekh the Destroyer, not a Transcendental Being, but an insanely powerful alien, who had power comparable to one. The Doctor stated that even the Time Lords wouldn't be able to stop him if he escaped at full power
- Omega, one of the founders of Time Lord society, who had been trapped billions of years ago in a black hole leading to a universe of antimatter, which he learned to warp and control with his will, so much that even though his physical body decayed he existed as a creature of pure will, and was powerful enough to overwhelm the Time Lords before the Doctor defeated him
- The Celestial Toymaker, also known as the Crystal Guardian, one of the Guardians of Time, the embodiment of Dream and Fantasy
- The Black Guardian, another of the Guardians of Time, this one the embodiment of Darkness and Chaos
Including his feats in the EU, he also defeated The Grace
Also, time travel by itself is very easy to do for most races in DW, so being capable of it won't help you much. The simpler forms of time travel (like the time agents' vortex manipulators) are to a TARDIS what a bicycle is to a space shuttle.
Finally, the Doctor actually has canon plot shields, in other words, the universe and all of the laws of reality will generally conspire in his favor. This is actually the explanation given for why enemies tend to always miss when shooting at him.