DVD Decrypyer - Kinda obvious what it does...
DGIndex - Generat d2v file.. wont go into detail...
YATTA/YMC - Decimating and IVTC. (and vfr blah blah blah)
Avisynth - Filtering, etc.
MeGUI + xvid_encraw or x264 - actual video encoding
Aegisub (and sometimes Subtitle Workshop) - Subtitle Editing, Timing/Timeing Fixes, Typesetting.
VirtualDub(Mod) - I ONLY use this for the initial lossless filtered encode (usually lagarith) and in Fast Recompress mode (cant be too cautious with vdub.. D:)
Adobe Audition - Audio fixes, if required.
LAME - If i'm usign mp3 audio.. this is the encoder to use..
OggEnc32 - Vorbis encoding.
FAAC - I RARELY use this, but i SOMETIMES used to for aac encoding...
BeSweet - Vorbis (depends) and AAC (With Nero's DLLs)
mkvmerge + mmg - Muxing matroska files, of course.
AviMUX GUI - If I, for soem unknown reason, HAVE to use teh avi container, this is the muxer to use.
Graphedit - DirectShow encoding (RARELY) and muxing native mpeg4/asp into the matroska container if im too lazy to use xvid_encraw to output mkv (aka if i forget, blame laziness :P) (via haali matroska muxer)... (screw vfw compatability >_> iso standards ftw...)
HkSFV - Generate md5 and crc checksums.
Various Avisynth Plugins - OBVIOUS.
mkv2vfr, avi_tc, etc - for use with pre-encoded files like the evil 120 fps (hack) encodes japenese cappers love ever so much, ec.
SubRip - OCR Subtitles.
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Inverse Telecine.
I usually use YATTA/YMC and work with teh d2v file. It would be a huge pain in teh ass to have to describe everything i do in YATTA here... so i'll simplify it... open the d2v in YMC and configure it, run it through, open in YATTA and work with it (switch, pattern guidance, freezeframe , post process, etc etc. all are on an "if it needs it" basis). Output the avisynth script, take teh parts i need, etc.
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Variable Frame Rate.
DVD: I use either YATTA or TDecimate to process it depending on te source. Mux the mkv with thr timecodes file etc. Use aegisub to generate a correct (vfr aware) subs file with the timecodes etc.
DTV: use mkv2vfr or avi_tc to generate a decimated file and timecodes.
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Main Ones
XviD (via vfw or xvid_encraw.exe, but i much prefer xvid_encraw) (mpeg4/asp)
DivX (but seriously? why use DivX?) (mpeg4/asp)
H.264/AVC/MPEG4 Part 10 - Via x264.exe, encavc.exe (ateme's encoder (old)), Nero Digital AVC (Ateme's encode as well). I prefer x264 for various reasons. CoreAVC's promised AVC encode looks to be interesting too. :)
I also know how to use lesser known ones, but that isn't really important here.
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What I use to filter anime can differ GREATLY, depending on how clean the source is and how well mastering was done. I regularily use deblockers, denoisers and/or smoothers (spatial and temporal), debanding filters/scripts, sharpeners, and other evil things.. depending on the source. I guesss you can just ask me in person if you need more info....
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Vorbis - via besweet or oggenc32
AAC (HE and LC) - via besweet + nero's aac dlls (or faac... but nero's dlls are better)
MP3 - via LAME
MP2 - via besweet (but who in their right mind uses mp2?!)
Various lossless formats - Only useful for concert dvds.
If available, I may mux in studio ac3 or dts audio.