The question possibly could be broken down into a couple other questions:
1. What hydrology method is used to compute design flows (Rational, SCS, SWMM Runoff, etc.)?
2. What hydraulic method is used to calculate depths/water elevations? (uniform flow computation for each pipe segment, steady-state backwater analysis using energy equation, dynamic routing using SWMM or similar)
3. What computer software or manual method is used to do the above?
In my opinion, the most uncertainty surrounds question 1, the design flows. I agree with cvg that the Rational Method is not necessarily conservative - most side-by-side comparisons of flows calculated using the Rational and SCS methods that I've seen have higher flows from the SCS method. Rational Method seems to more closely match gage flows / actual catchment data without much conservatism, which is a good or bad thing depending on your situation and how you account for variability/factors of safety. Granted it all depends on your procedures for calculating input parameters.
Item 2, hydraulic method, sometimes is quite important and sometimes makes little difference. When you're designing a new system without a significant downstream backwater and can design in adequate freeboard, probably all methods will work well if used properly. But when you've got backwater effects, hydraulic restrictions, intentional or unintentional storage in the system, you need a more detailed analysis.
With regards to item 3 Computer Software, something that has puzzled me is that in a field where so many of the industry-standard water resources software is government-developed freeware (TR-20, TR-55, HEC-HMS for hydrology; HEC-2 and HEC-RAS for river hyraulics, HY8 for culverts, SWMM for dynamic hydraulics), steady state sewer modeling is the one big application where no government agency has stepped in with a widely-used, Windows-based software, something along the lines of StormCAD (I consider SWMM to be in a separate category). I guess the government has never felt the need for a public-domain application of this nature (though let me know if you know about one). Good thing for Haestad and the other software vendors. Maybe it's because it's possible to do the core analysis in a spreadsheet?