Hello, I have heard that Freespace was the best space sim around, but I am curious as to whether I should start with the first one or just skip to the second?

Both parts are great. Many find FreeSpace 1 story superior. There is a mod for FreeSpace 2 called FS1 port which gives you all FS1 content + FS2 graphics and other improvements. Start with first part of series, whether by installing original FS1 game or port for FS2 - it doesn't matter.

Controls and gameplay in both games are basically the same.

Look at recent topics for more info.

Be sure to install Freespace 2 Source Code Project (aka SCP or FSOpen) for FS2.

What does SCP add? Also, what is the name of the "FS1 in FS2" mod? I cannot seem to find it.

Source Code Project is the next step in FreeSpace series evolution. Graphics of FreeSpace 2 are vastly improved, added support for higher resolutions, large textures, lightning, shadows... Added support for mods (including custom ships and armament, community made campaigns and maps). The most notable mod for SCP is FreeSpace 1 conversion and its expansion (again, improved by community) Silent Threat: Reborn.

FS2 SCP on Wikipedia

FS2 SCP installation guide

Main site + screenshots

FS2 SCP just looks and feels awesome. FS2 was released in 1999 but with SCP it looks like a recently released game.

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FS1 port is just called FS Port. :')
http://fsport.hard-light.net/website/
http://www.hard-light.net/wiki/index.php/FreeSpace_Port

More info about story and installation of FreeSpace 1 Port on FS2 SCP can be found here
http://www.gog.com/en/forum/freespace_series/a_question_about_freespace_story

FS1 is a good, solid space shooter and well worth playing. FS2 is the daddy of all space shooters, but you'll appreciate the story more if you've played through the first one.

I really love both of them. So much.

You should play the first series of FreeSpace first before second.