I use something like 99 up front and then do a more classic registry number, ala 991701 (though not that number specifically, I think my main's ship is 991974? I'll have to double check, it's been awhile since I paid attention to my number).
Most of my ships are named after historical events, people or characters, so I try to write my NCC/NX to something corresponding to that ships name. For Example, al my USS Yamatos (for each character) are either NCC or NX 741945, which roughly translates to to 7 April 1945, the date of her sinking
Really wish I could drop that last 4 though so it'd be a little more in line with when the Excelsior class was actually being constructed since the lore for the Tiburon has her sitting now at 77 years of service