Sounds like something I always do.
Don't mean to echo, but what Connor said.
I, however, don't like MKVmerge as MKV files made from it won't play in Divx Video player. Plus, if it was to be uploaded on FailTube, the audio and video won't be synced (from my experience with uploading Cocorin on cubex and ZX on my personal channel).
What I do is use MKVmerge to make my one whole file, extract the video and audio fiile (h.264 and .aac), and then remux them in MeGUI. That is what I did with Valkyrie Profile: Lenneth and Chrono Trigger.
Also, AviSynth has a trim option for "cutting" out parts (it is more like "display these frames"). I find it very easy to use. Use VirtualDub to find the frames. VirtualDub can also also "read" AVS files (drag and drop).
Dunno if this will help, but here is what I use for trimming:
e1=trim(x,y)
e2=trim(x,y)
e3=trim(x,y)
e1 + e2 + e3
X is the where you want to start and Y is where you want to stop. Say I want to display frames 234 to 43210. That will be e1=trim(234, 43210). The E1 plus E2 etc are to bring them together. You can also add stuff like dissolve and Fade in and Fade out.
Example of what I used for my [hopefully acceptable] Ape Escape 3 Longplay:
e1=trim(500, 20250)
e2=trim(21005, 86560)
e3=trim(87405, 178430)
e4=trim(179795, 361980)
e5=trim(377280, 505545)
e6=trim(511860, 538325)
e7=trim(539225, 666765)
e8=trim(680855, 723205)
e9=trim(733310, 762120)
e1 + e2 + e3 + e4 + e5 + e6 + e7 + e8 + e9
That is pretty much all 5 Ape Escape 3 clips put together and "edited".
How about a somewhat complicate one from doing Parasite Eve on a PSP with RemoteJoyLite:
e1=trim(400, 23560).crop( 80, 24, -82, -24).LanczosResize(640,480)
e2=trim(23561, 25500).crop(80, 22, -80, -16).LanczosResize(640,480)
e3=trim(25501, 32325).crop( 80, 24, -82, -24).LanczosResize(640,480)
e4=trim(32326, 33635).crop(80, 22, -80, -16).LanczosResize(640,480)
e5=trim(33636, 58054).crop( 80, 24, -82, -24).LanczosResize(640,480)