Edited to talk about 'show type'.
I have an i3-4130T (35 watts woot!) with 4 gb ram and a single 1TB HDD and I use MCEBuddy 2.13 (the last free version) to convert for my Roku 3 played via Plex. FYI I use the free Plex channel.
First, a note about doing it 'automatically': With plex it's best to keep movies and TV shows in separate folders. If the 'Thor' movie is in my TV Shows folder, Plex will think it's a 1980's cartoon. You need to make a 'movies' folder and a 'TV' folder for Plex. You need to make two conversion tasks in MCEBuddy. They can be identical, except for one difference: in one task, under advanced settings set 'show type' to 'movies' and set the destination to your 'movies' folder'. In the other task, set 'show type' to 'shows' and set the destination to your 'TV' folder. This way, everything is available on the Roku without intervention. I have never used the 'show types' setting, I just learned about it while responding to your post.
Of course, you can set up those two conversion tasks with other differences, as I describe below. Personally, I don't have my shows convert automatically. I plan in deleting some shows as soon as I watch them, and I watch them through WMC, so I don't want to use the resources needed to re-encode them. I have folders named 'Convert me TV MP4' or 'Convert me Movies MKV' and I cut/paste programs into those folders when I want them reencoded. Then I have separate conversion tasks that watch for files in specific folders, convert them to the desired format, and save them to the correct folder for Plex. But now that I know about the 'show types' setting, I may choose to do things differently for a completely automated system. Also check off 'Rename and Sort by Video Information' and 'Use MC Compatible Naming' so the files will be named and saved for Plex or XBMC.
I use the MP4 High Quality profile and I DO NOT select the 'Multi channel' audio. I set the width to about 1400 (I forget exactly). This creates MP4 files with 720P h.264 and stereo
AAC audio. If the broadcast was in 5.1, it will be re-encoded to stereo. I do this because the Roku and my kid's iPad can natively play this format without forcing my PC to transcode on the fly. The iPad can only handle MP4 with h.264 and AAC (no MKV and no AC3), and the Roku can either handle MP4 with h.264 and AAC stereo, or MKV with h.264 and AC3 multi-channel audio, but the Roku can NOT natively play MP4 with AAC 6 channel (5.1) audio. The Roku may be able to handle other container/audio formats, but those two work for me.
If I want surround/5.1 audio (i.e. dad's action movies), I convert them to MKV and I select 'multi-channel audio'. This creates MKV files with 720P h.264 and 5.1
AC4 audio.The Roku will then play the file natively without transcoding on the server, and I get surround sound explosions, but the kids can't watch it on the iPad unless they transcode.
Going from a WTV file to a MP4 takes at least twice as long as the program length. 2 hours for a 1 hour show is on the fast side for my system, but then again my system is designed to be cool and quiet. I will check my logs tonight and get back to you. I set the MCEBuddy priority to 'Medium'. It makes WMC a little sluggish but I mostly use the Roku for the front end so a sluggish PC doesn't matter. I have a single HDD for storage. A second HDD and a system SDD are on my wish list. When transcoding my CPU usage is about 90%, disk queue length is 0.1 or less, and out of 4 GB memory I have about 1.5 gb available so it's fair to say that the CPU is the limiting factor in my build. I have a SD HDHomerun Prime and my computer has recorded 2 TV shows while MCEBuddy is re-encoding on that same single HDD with no problems. If I set the priority to low, a half-hour show might take 6 hours.
FYI if I encode to a MP4 with h.264 and AAC stereo
audio, CPU utilization is about 1-3% when Plex is serving up the file to the Roku, programs start playing very fast on the Roku, and I can use the Roku remote to very quickly skip ahead through commercials. If I press the right side of the 'cross' on the remote, the program will skip ahead 15 seconds (or whatever amount of time) and resume playing in about a second; or if I press to the right 6 times, it will advance 1 1/2 minutes and resume playing almost instantly, etc.
But if I encode to a MP4 with h.264 and AAC 5.1
audio, CPU utilization is about 90% (2 cores/4 threads) when Plex is transcoding/serving up the file to the Roku, programs take several seconds to start, and using the Roku remote to skip ahead through commercials is painfully slow. Audio is also very poor. And I'm afraid that if my computer tries to record 2 or 3 programs while transcoding on the fly, a show may not be recorded.