Aside from the Dana differential covers, the biggest difference between the axles is the size. The number in the name (Dana 30, Dana 44, etc.) is in reference to this.
Dana 30: This axle size is the most common, and you'll only find it on the front of Jeep. They have a ring gear diameter of 7 and 1/8 inches. The Dana 30 gear ratios are either 3.21 or 3.73. The width of the axle shafts is 1.13 inches.
The YJ Dana 30 hold a reverse cut ring and pinion, but the TJs do not. Both TJs and YJs, however, use a 5x4.5 inch bolt pattern.
Dana 35: This was an axle size used on most Jeep rear axles. They had a ring gear diameter of 7 and 9/16 inches. They came with either a 3.21 or 4.10 gear ratio. The width of the axle shafts is 1.13 inches.
Dana 44: These are the beefier axles found on the rear of all Wrangler models now with either a 3.21 or 3.73 gear ratio. The Dana 44 ring gear size is 8 ½ inches. Rubicon models come standard with a 4.10 rear gear ratio and also use a Dana 44 axle in the front with either a 3.73 or 4.10 gear ratio. The width of the axle shafts is 1.31 inches. Rubicon models also come with an electronically lockable differential for optimal traction while in 4WD.
Keep in mind not all Dana 44s are the same. JK Rubicon models have a thicker, slightly redesigned 44. This Rubicon axle is referred to as a Super Dana 44.