ENA for SMART offers a comprehensive set of analyses but is restricted to SMART type surveys. I think it works well for most people. Components such as calculating z-scores (e.g. HAZ, HAZ, WAZ) can be done using other software such as STATA or R. The WHO provide a set of "macros" for a wide range of software (R, STATA, SAS, SPSS) and their. Some of these "macros" will do a complete survey analysis report (as does ENA for SMART). They also have standalone tools such as as WHO Anthro and web-based tools such as the WHO Anthro Survey Analyser for calculating z-scores and making survey reports like ENA. Tools for sample design are available but are not usually as closely aligned to SMART designs as ENA fro SMART is. An R library, developed for NIPN, is available that provides equivalent functions to those used in ENA's data quality assessment tools. Analysis of survey data needs to account for the sample design. ENA does this for SMART designs. STATA, SAS, SPSS, and R have functions / libraries for analysing data from complex sample surveys but these can be complicated to use. I doubt that there is a single tool that covers all of what ENA for SMART provides as an "out of the box" solution. I use R and R-AnalyticFlow for most data analysis. I used to use the older MSDOS EpiInfo for working with nutritional anthropometry survey data. Newer versions of EpiInfo provide useful tools for working with nutritional anthropometry survey data.
I agree with Woody that the "black box" tools may not provide what you want. They do a good job for a SMART survey because it is a standardised approach with a standard analysis and report but the analysis is limited. Once you move away from standard SMART you will need to use a statistical packed and that may require considerable espertise to use well.
I hope this is of some use.