And I thought I already had a nice, nearly-complete guide... In the newer version, the interface has been rearranged quite a bit, so some things will be different from what you were used to. When you run the installed emulator, you'll have five options to choose from, none of them are exactly self-explanatory.
Run / Configure CD in Drive
Here, you can select which CD drive you're going to read the game from. Setting the region is important. If you get the "Game disc not suitable for this system" error, that is what you'll need to adjust. The Force Region option won't do anything, since you can't patch a read-only CD to another region. The Auto-choose CD-ROM Region option doesn't seem to work either. Read on, and you'll know the other reasons why playing from an image file is much more favourable.
Run Saturn Image / Configure
Load Disk: In the left side you can see a directory selector, and your favourite directories. You can save/remove favourites, but there isn't much use to this if you keep all your games in one directory. The Change BIOS button doesn't seem to work, and it's obsolete anyway, there's another option for changing the BIOS file. The edit ActionRplay.ini lets you edit the language files. The Edit Conf.ini button does just that, let's you edit that file. This was previously named BASE.INI, storing data on the game to be played. It's probably unused now, since there isn't even need for an extracted TOC anymore. So, once you've set everything up, double-click the image file in the lower left, and after displaying some messages in the window to the right, the game should start. Simply single-clicking the file will only display some useful info on the game, like region, name, ID, and release date. This is pretty much the same as the CUE / BIN Info option under Tools in the previous versions.
Action Replay: This new option allows you to add cheats and hacks, and search for them. As of this writing, I couldn't get built-in codes to work, searching did seemingly nothing. So, if anyone can provide a method to use this part of the program, I'd be grateful.
Configure Cassini: Select the resolution, whether you'd want it to be fullscreen, select language of the menus, and configure the controls for player one. Take note that you'll have to double-click the gray boxes to be able to change the associated button. This works fine with one player, but I recommend using the old configuration tool, Configure.exe to set up the second player. By using the Edit User.ini button, it's possible to set up two players with gamepads, but I can't try this out, so the theory will only be added on demand.
Cassini Tools
Country Code Changer: It's the good old satconv.exe, use it to change the region of a game if you have trouble playing it. (You might need to patch the game to European to play it with a European BIOS, and so forth)
Cue Maker: Runs the segacuemaker.exe in the Tools\CueMaker directory under the emulator's main directory. This has little use this way, refer to the guide above on creating CUE sheets for Saturn games with this tool.
Install SFPI/ASPI: Installs ASPI drivers for your CD drive... You might consider doing this if the emulator reports read errors for no obvious reason. Provided you use CUE/BIN files instead, you won't need this option.
Get Saturn ID: Drop a BIN file of a Saturn image into the text box and it will extract it's unique identifier. More on this in the Miscellaneous section of this guide.
Create CD Image: Uses the ASPI drivers you can install with another option to dump an image to hard drive. You'll only be able to select a drive by entering that three-number code the check button provides you. After that, select country, and enter the directory and filename, without extension, where you want the file to be created. This will leave you with an ISO, CUE, TOC.BIN and BASE.INI files. I guess the latter two aren't necessary anymore, since the emulator runs BIN/CUE images without problems, could be that this version auto creates those files from the image.
MP3 to Wave Converter: Converts MP3 files to WAV, so you'll be able to mount the ISO+WAV as a proper disc. Be sure to right click the Joblist window and set the Output Directory under Preferences to an existing directory, or the program will freeze.
Saturn Movie Player: A cool little Japanese movie player utility. I couldn't get all of the text to display properly in the menu, so I had little luck tweaking around the options. For some reason the movies didn't show up properly for me, though they converted to AVI nicely. A major bug was that the second half of the movies always got cut off.
Cassini ASM Code: Opens the Cassini.ASM in Notepad. Source code, all in Assembler. Get that stuff away from me. Seriously, you won't need this, unless you're a coder.
Debugger: A debug version of the emulator, not really meant for playing. Basically, if you're using this part of the emulator, you don't need this guide.
Audio Extractor: Extracts CD audio via the ASPI manager. You could do this with any other program that you'd normally use to grab audio CDs.
User Defined Script: This seemingly does nothing except run the User.BAT batch file in the emulator's directory. What could possibly be achieved by command line arguments is beyond my knowledge, as no such functions are documented... In other words, this seems useless so far.
CD ID & Ripper: Has the functionality of a basic version of CDMage. It allows you to scan an image for errors, possibly repair them, and also extract data from images. You could use it for trying to fix corrupted image files, I suppose.
Cassini BIOS
You'll have six buttons for choosing a BIOS. What this does, is extract the BIOS files from the archive in the BIOS folder, and put the selected one in the emulator's main directory as CASS.BIN. So, if you want to use your own BIOS file, simply put it in the emulator's directory and rename it to CASS.BIN.
Cassini Help
This section contains some semi-useful help files, but I believe these forums would be a better source of information in all of those areas. The Cassini ASM button opens up the Cassini assembler source in Notepad. In other words, don't waste your time here.
Miscellaneous- Sound lagging in movies and transparency seem to have been improved in this version. If you have such issues with an older Cassini, give this a try.
- The Games.dat file stores the hacks for games. You can add your own entry just by mimicing any other entry, putting the Saturn ID of the game of your choice in the brackets. The lines starting with a semicolon are just comments. So, if your game is showing graphic corruption that a similar game doesn't, you could try checking if there is an entry for said game. For example, only the japanese version of Guardian Heroes had some hacks installed in the Games.dat file, copying that under the ID of the US game will fix some graphics issues.
- Running in low resolution is more favourable in the case of some games. For example, Radiant Silvergun uses a line to inform you on the health of boss enemies. What sucks is that this line is always 1 pixel wide, which means it will barely be visible in any resolution higher than 320*240.
- You can use some function buttons during play to modify certain settings. F4 shows you the framerate, F10 lets you pause the emulation. F3 changes layer priority, and the numbers 1-6 let you turn individual background layers on and off, the button 0 switches sprites on/off. These can come in handy where some of the graphic features isn't emulated correctly, for example flying through the dark spiked room in Dracula X.
- By tweaking the VSync, CDWait and FrameWait values in the Games.dat for a game, you can sometimes gain a lot of speed. The tradeoff is compatibility, and the drawback to this method is that this still won't rid you of slowdowns. In some situations, the emulation will be sluggish, no matter what.
- If all else fails, try updating your video/audio/gameport drivers, including Direct X, it never hurts. The emulator WILL run crappy no matter how fast your machine is (certain games are an exception), and there's little you can do to make it run faster.
Thanks go to SegNin, Myst, LordOfTheCynics, and everyone else who contributed to this guide!