Simple command line utility for merging spreadsheets and addings some formatting. There are bugs and some exceptions are not handled gracefully, in my case it does what I need so here's some scissors, start running. Needs Excel 2010+ and .Net 3.5.

join-spreadsheet.cs

using System;
using System.IO;
using System.Linq;
using Microsoft.Office.Interop.Excel;

/* Simple command line utility for merging spreadsheets and
 * addings some formatting. There are bugs and some exceptions
 * are not handled gracefully, in my case it does what I need
 * so here it is.
 *  -Sean McArdle
 */

namespace JoinSpreadsheet
{
    class Program
    {
        static void Main(string[] args) {

            // Check for any arguements
            if (args.Length == 0) {
                ShowHelp("You must pass a filename");
                Environment.Exit(1);
            }

            // Show full help            
            if ((args.Contains("-h") ||
                args.Contains("--help") ||
                args.Contains("/?")) &&
                args.Contains("--full")) {
                ShowHelp(null, true);
                Environment.Exit(0);
            }

            // Show standard help
            if (args.Contains("-h") ||
                args.Contains("--help") ||
                args.Contains("/?")) {
                ShowHelp();
                Environment.Exit(0);
            }

            // Check for arguments
            if (args.Length < 2) {
                ShowHelp("You must pass a filename");
                Environment.Exit(1);
            }

            // Load workbooks
            var excel = new Application();
            excel.SheetsInNewWorkbook = 1;
            excel.Visible = true;

            _Workbook master = (_Workbook)excel.Workbooks.Add();

            // Enumerate arguments
            int s = 1;
            for (int i = 1; i < args.Length; i++) {
                string p = args[i];

                if (File.Exists(p)) {

                    WriteDebug("Opening input file: {0}", p);

                    string path = Path.GetFullPath(p);
                    var wb = excel.Workbooks.Open(path);

                    // Enumerate worksheets
                    foreach (Worksheet ws in wb.Worksheets) {
                        ws.Application.ActiveWindow.SplitRow = 1;
                        ws.Application.ActiveWindow.FreezePanes = true;
                        if (ws.Rows.Count > 0) {
                            // Freeze first row and apply auto filter
                            Range fr = (Range)ws.Rows[1];
                            fr.Activate();
                            fr.Select();
                            for (int j = 1; j < fr.Columns.Count; j++) {
                                try {
                                    fr.AutoFilter(j, Type.Missing, XlAutoFilterOperator.xlAnd, Type.Missing, true);
                                }
                                catch {
                                    break;
                                }
                            }

                            Range last = ws.Cells.SpecialCells(XlCellType.xlCellTypeLastCell, Type.Missing);
                            Range cells = ws.get_Range("A1", last);
                            cells.Columns.AutoFit();
                        }
                        ws.Copy(Type.Missing, master.Sheets[s]);
                        s++;
                    }

                    wb.Close(false, Type.Missing, Type.Missing);
                }
                else {
                    var c = Console.ForegroundColor;
                    Console.ForegroundColor = ConsoleColor.Red;
                    Console.WriteLine("File: {0} does not exist, check path.", p);
                    Console.ForegroundColor = c;
                }
            }

            if (excel.Workbooks.Count == 0) {
                Console.WriteLine("No workbooks loaded, exiting...");
                Environment.Exit(0);
            }
            else {

                ((Worksheet)master.Sheets["Sheet1"]).Delete();

                // Determine report destination
                string name = (Path.IsPathRooted(args[0]))
                    ? String.Format(@"{0}", args[0])
                    : String.Format(@"{0}\{1}", Environment.CurrentDirectory, args[0]);

                WriteDebug("Report name: {0}", name);

                // Save report and close excel
                string extension = Path.GetExtension(name);
                XlFileFormat fmt = XlFileFormat.xlOpenXMLWorkbook;
                switch (extension.ToLower()) {
                    case ".csv":
                        fmt = XlFileFormat.xlCSVWindows;
                        break;
                    case ".ods":
                        fmt = XlFileFormat.xlOpenDocumentSpreadsheet;
                        break;
                    case ".xls":
                        fmt = XlFileFormat.xlWorkbookNormal;
                        break;
                    case ".xml":
                        fmt = XlFileFormat.xlXMLSpreadsheet;
                        break;
                    case ".html":
                        fmt = XlFileFormat.xlHtml;
                        break;
                    default:
                        // do nothing, stick with OpenXML
                        break;
                }

                WriteDebug("File extension: {0}  output format: {1}", extension, fmt.ToString());

                master.SaveAs(name, fmt);
                master.Close();
                excel.Workbooks.Close();
                excel.Quit();
            }
        }
        
        private static void ShowHelp(string msg = null, bool full = false) {

            if (msg != null) {
                Console.ForegroundColor = ConsoleColor.Yellow;
                Console.WriteLine(msg);
                Console.WriteLine("\n");
                Console.ResetColor();
            }

            Console.WriteLine("Summary:");
            Console.WriteLine("    merge_csv.exe merges worksheets from different spreadsheet");
            Console.WriteLine("    formats into a single master workbook.");
            Console.WriteLine("");
            Console.WriteLine("Command usage: ");
            Console.WriteLine("    merge_csv.exe <merged spreadsheet> <input sheet> [additional sheets]");
            Console.WriteLine("");
            Console.WriteLine("    Argument 0 and 1 are required and may be relative or absolute paths.");
            Console.WriteLine("");
            Console.WriteLine("Example: ");
            Console.WriteLine("    merge_csv.exe master_report.xlsx foo.csv bar.xls baz.csv");
            Console.WriteLine("");
            Console.WriteLine("Switches:");
            Console.WriteLine("    -h, --help, /? : show help");
            Console.WriteLine("      Adding --full qualifier shows command symantics.");
            Console.WriteLine("");

            if (full) {
                Console.WriteLine("Symantics:");
                Console.WriteLine("    If the merged spreadsheet path is relative and not \"rooted\", path");
                Console.WriteLine("    contains a \\ to specify location relative to current, the path is");
                Console.WriteLine("    resolved to be the current location of executing shell; not the default");
                Console.WriteLine("    excel path (usually Documents) or location of merge_csv.exe.");
            }
        }


        private static void WriteDebug(string msg, params string[] subs) {
#if DEBUG
            WriteDebug(String.Format(msg, subs));
#endif
        }

        private static void WriteDebug(string msg) {
            Console.ForegroundColor = ConsoleColor.Cyan;
            Console.WriteLine("Debug: {0}", msg);
            Console.ResetColor();
        }
    }
}