for capturing video from a PS2, or a PC w/ s-video, ALWAYS USE MPEG2. I REPEAT.
ALWAYS. USE. MPEG2. (don't confuse it with MPEG4)
Why? #1 reason, because it is used to capture interlaced video streams. If you use ANYTHING else, microsoft AVI, DIVX/XVID, or MPEG4 or H264, you will destroy the interlacing data, no matter how high of a bitrate you set. DONT use MPEG4 as your capture codec, unless youre using a mac, it's a bitch codec to work with.
i dont know of any PC's that can compress MPEG4 in real time anyways, I'd use Component Video from your console instead but S-Video is ok if your card/console doesnt support Component. Most lossless codecs and Uncompressed AVI support Interlaced video and can be deinterlaced with no problem. With HDTV being the future and HD consoles Progressive is the way to go anyways its much higher quality than Interlaced plus theres no issues between PC and TV.
For capturing with capture card you can use Virtual Dub(newest version whcih is like 1.7.8 or something, also NOT virtual dub mod.) and capture to uncomressed AVI. I would also recomend a lossless codec instead of uncompressed AVI, Lagarith is really good and so is Huffyuv. I personally like Lagarith because its faster, Huffyuv is fast encoding but it decodes slowly so if you have to edit it its going to be troubble. You shoudl also be able to export to them using your editing software once they are isntalled.
Settigns depend on what you want from compression and codec you use, if you want smaller files use H264 2pass, h264 is better than Xvid in low bitrate situations(prettymuch anything under 10k bitrate is low bitrate).
For h264, export raw AVI then use Megui(its got nice profiles you can use if you dont know anything about setting up the encoder) to encode to h264 and put it into an .mp4 container, for Xvid you can use whatever your editing programs compressor is, and AVI container obviously. 2pass is allways the way to go for both really.
Personally i use between 1000 and 3000 for VBR bitrate and 60 FPS, i try to keep matches around 100mb, you can use less if your encoding 320x240 for youtube(becuase youtube butchers your video anyways, its random luck when their encoder decides to not trash the video you upload).
Other random tips. . . When capturing from a capture card, capture in YUY2 or YUV or YV12. Theres no reason to not use H264 for your final compression, unless ofcource you plan to play it back on computers from 10 years ago. You can make video more compressable by using the correct filters(however if you use fraps there probably wont be issues with the video, but capture cards there is noise and other artifacts in there that could be cleaned up). Have Animeruko do youre video encoding for you when hes not buisy complaining about something.