Convert .pem and .pub to .pfx file

Your keys may already be in PEM format, but just named with .crt or .key.

If the file's content begins with -----BEGIN and you can read it in a text editor:

The file uses base64, which is readable in ASCII, not binary format. The certificate is already in PEM format. Just change the extension to .pem.

If the file is in binary:

For the server.crt, you would use

openssl x509 -inform DER -outform PEM -in server.crt -out server.crt.pem

For server.key, use openssl rsa in place of openssl x509.

The server.key is likely your private key, and the .crt file is the returned, signed, x509 certificate.

If this is for a Web server and you cannot specify loading a separate private and public key:

You may need to concatenate the two files. For this use:

cat server.crt server.key > server.includesprivatekey.pem

I would recommend naming files with "includesprivatekey" to help you manage the permissions you keep with this file.

You could use BouncyCastle (assuming C#, because you mentioned .NET).

Let's say localhost.pem here contains both the certificate and the private key, something like this should work:

using System;
using System.Collections;
using System.Linq;
using System.Text;
using System.IO;

using Org.BouncyCastle.Crypto;
using Org.BouncyCastle.OpenSsl;
using Org.BouncyCastle.Pkcs;
using Org.BouncyCastle.X509;
using Org.BouncyCastle.Security;

namespace TestApplication
{
    class Program
    {
        static void Main(string[] args)
        {
            StreamReader sr = File.OpenText("localhost.pem");
            IPasswordFinder passwordFinder = new PasswordStore("testtest".ToCharArray());
            PemReader pemReader = new PemReader(sr, passwordFinder);


            Pkcs12Store store = new Pkcs12StoreBuilder().Build();
            X509CertificateEntry[] chain = new X509CertificateEntry[1];
            AsymmetricCipherKeyPair privKey = null;

            object o;
            while ((o = pemReader.ReadObject()) != null)
            {
                if (o is X509Certificate)
                {
                    chain[0] = new X509CertificateEntry((X509Certificate)o);
                }
                else if (o is AsymmetricCipherKeyPair)
                {
                    privKey = (AsymmetricCipherKeyPair)o;
                }
            }

            store.SetKeyEntry("test", new AsymmetricKeyEntry(privKey.Private), chain);
            FileStream p12file = File.Create("localhost.p12");
            store.Save(p12file, "testtest".ToCharArray(), new SecureRandom());
            p12file.Close();
        }
    }

    class PasswordStore : IPasswordFinder
    {
        private char[] password;

        public PasswordStore(
                    char[] password)
        {
            this.password = password;
        }

        public char[] GetPassword()
        {
            return (char[])password.Clone();
        }

    }
}

You'll probably need something a bit more subtle for the IPasswordFinder and if you want to handle certificate chains correctly. For more advanced features, you may be able to find more details in the BouncyCastle examples.