Ok, now I've been to alot of forums (mostly archives) about Gundam vs. Eva and I'm dissapointed with the horrible bias based on opinion. I am one of those rare people that likes both Eva and Gundam. First of all Evangelion has things seen only in japan release games, things like the Trident land cruisers (Girlfriend of steel, a PC game). Tridents are bigger than Evas and the basic model has a 100mm machinegun on its chin (Zaku's have a 120mm rifle). Later on these have large railguns or positron weapons (they are made to kill Evas). While not going into details on the JSSDF, Angels, or SEELE, the eva's have many advantages in combat. Recoil for one, Eva's are fleshy so they absorb recoil while gundams and MS's feel more shock from it (Eva's can use larger weapons). The Evas also have common knowledge advantages such as AT fields, so in a fair 1-on-1 fight the Evas have the advantage. Evas are also bigger (about 2x the size) than a gundam/MS.
While avoiding too much detail on Evangelion and its expanded universe I will explain Gundam. There are 15 Eva units I currently know about, while there are thousands if not millions of Gundams and MS's thus giving a serious numbers advantage. Gundams have pilots of the same skill if not better than Asuka (her Eva won't listen in the show but the movie shows her true skills). While the weapons are not superior the numbers of machines with skilled pilots are (Char, Amuro). In a sudden attack using just MS's on NERV HQ they would have an excellent chance of success in at least killing the pilots. MS-18E Kampfer is a fast attack MS (0080) that wreaks havok with speed and firepower, so a blitz on NERV HQ would give them the upper hand. Using Terrain, Skill, and Tactics, Gundam could beat Evangelion without actually fighting the Evas or the N^2 happy JSSDF. For those that think Gundams and MS's could mass in space, Eva's have equipment allowing them to fight in space (expanded universe that includes the games, both tabletop and video games). The JSSDF could possibly slow a blitz of MS's and Gundams but only slow it not stop it. The mass of JSSDF seen in End of Evangelion had days to gather due to NERV being on high alert and nobody going outside to see them preparing.
In an obvious attack by Gundam, Evangelion would win.
In a well planned and prepared blitz, Gundam would have a good chance of winning.
(I just want to see Heero vs Misato in a gunfight, that would be epic)
Evangelion: Anima (Newtype Magazine) featured things like Jet Alone Prime (JA-P). It is far superior to the original JA (Jet Alone) and escaped NERV sabotage. Then there are the other equipment types for the Evas, like the F-type, A-type, and E-type equipment.
This however does not include content the new Rebuild of Evangelion films.
Still, neither is superior to the other, circumstance determines the victor.