Without no doubts, a researcher should several nice tools to handle their data, and testify their results. EXCEL, SPSS, and R represent different stages for doing a research.

Most data retrieved from a database has a excel format like xls or xlsx. We probably spend lots time on cleaning missing values and doing some simple valuable transformations with EXCEL.

What is great about SPSS is that it provides the most direct interface for storing your raw data. Consider SPSS as a extension of EXCEL. It allows the definition of a variable could be stored directly in SPSS format dataset. This will be extremely useful if you are collecting data from surveys.

3. R
The preceding tools provide you with the basic method for analysing your data. On the other hand, R is a powerful statistical language,also suggested by an article from Nature, for analysing more difficult problems. Once you know how to write a function in R, it will save lots of time through avoiding clicking the buttons in the above tools. Data visualization for your data is also a great advantage of R especially using its package, ggplot2. See the examples from Rstudio.

This article will continuously be updated and I welcome anyone of you to post your experience here.
These concepts will involve the definition of technology, functional form, and other matters especially some important theories in micro-economics. These are the fundamental assumptions when developing the methodology of efficiency measurement. My advice is that read Intermediate Microeconomics_A Modern Approach (8th ed), (Ch. 18, 19, 20, 21) or Microeconomic Analysis (3rd) (Ch. 1~6, 12, 26, 27) and then study very carefully about how to estimate these functional forms especially considering their error sources (these are detailed in the book chapter, A Survey of Functional Forms in the Economic Analysis of Production.) If you want to know how to estimate these in practice, the lecture note, Introduction to Econometric Production Analysis with R, is really worth reading since it combines all R codes and data.

Other suggestions are also listed as follows. Carefully read these references in the following order (words in the parentheses indicate the suggested sections).

Production, cost, profit function
Intermediate Microeconomics_A Modern Approach (8th ed), (Ch. 18, 19, 20, 21)
Microeconomic Analysis (3rd) (Ch. 1~6, 12, 26, 27)
Microeconomic Theory (Ch. 5)
Applied production analysis: a dual approach (All)

Distance function
Multi-Output Production and Duality: Theory and Applications

This article will continuously be updated and I welcome anyone of you to post your experience here.