mkvmerge should be fairly simple to work with, you just add the video (and audio if it's a separate file) and subtitles, set track options like language if you want, and mux. There's also stuff like chapters or attaching fonts, but I can't say I've actually used those yet.
Still, the latter should be fairly simple and the former is just an extra.
For encoding to H264 before muxing if the source's size is too big for your needs, Avisynth + MeGUI is what I use, but be aware that it probably has loads of stuff you may never use and be unnecessarily complex for that reason (not that it's really complicated once you know how it works). I'm not familiar with standalone encoders so you may want to wait for other suggestions.