The .30-06 was the first of the -06 series.
It started as the U.S. military's .30-03, or .30 Caliber cartridge of 1903. This was the replacement of the .30 U.S. Army cartridge, also known as the .30-40 Krag. An Ordnance Board change to a lighter spitzer bullet and cartridge neck length was completed in 1906, hence, the now-famous .30-06.
Wildcats developed from the .30-06 kept the -06 as a reference to the cartridge's parent case. Some wildcats were eventually taken up into production by the gun and ammo manufacturers, and "legitimized". The .25-06 is one of them. Others include wildcats like the 6mm-06, 6.5mm-06 (my long-range favorite), .277-06 (AKA .270 Winchester), 7mm-06 (AKA the .280 Remington), .31-06 (common in rechambered 7.7mm Jap Arisakas), 8mm-06 (common in rechambered 8mm Mausers) on up the chain, including the .35-06 (AKA .35 Whelen).
When wildcats were based on the .308 Winchester, they often, but not always, got a -08 suffix, hence the 6mm-08 (AKA .243 Winchester), 6.5-08 (AKA .260 Remington), 7mm-08, and so forth.