I think everyone probably has these thoughts at some point.
There are books/sites which recommend a bunch of "useful components" to have available. The only trouble is these things go out of date very quickly. For example the 741 and PIC16F84 are still being recommended in places even though they have both long (long long) since been surpassed.
If you know what is needed spec wise for your project (as you should do) then you can pick the components based on the specs. For example if you need 10MHz analogue bandwidth and you are using a 5V supply then you can filter opamp results accordingly. What speed does your uC need to run at 10MIPS? 40MIPS? what peripherals does it need? USB? SPI? CAN? Filter accordingly.
Parametric searches are your friend here (all the decent sites like Mouser, Farnell, Digikey, etc have them)
This applies to just about everything, so there's no quick way around reading through datasheets and making an informed decision (unless you already used the part of course)
So I would say the answer is probably to jump in head first and start learning how to use the search tools properly (look at any help available) picking your way through the components, read the datasheets, learn about what the specs/graphs/etc mean.
I certainly remember being overwhelmed by all the different options and long winded datasheets, but after a while your brain gets pretty good at filtering out the info you need quickly. Still takes time though, and is not the most enjoyable task.
Of course, if you're sure of the specs and you can get someone else to do it for you that's always a good option ;-)
Keeping up to date with new chips is useful too, I sign up for all the new product notifications for various places.
What's considered the maximum number of parts on a single page?
Depends on the size of the page. You can fit more on a D-sized plotter sheet than a B-sized (roughly A4) sheet. Don't crowd things to the point it gets difficult to read.
What to consider when making a schematic multiple pages?
Almost all my designs end up as multiple sheets. Sometimes the manufacturing guys cut them all up and paste them together in one big plotter sheet to make it easier to follow the signal flow. But normally I don't print out bigger than 11x17 so I work at that size.
Something you didn't ask: I tend to make the first sheet be the critical input and output connections of my circuit, and work up towards more complex circuits on later pages. Other people like to put the critical signal path parts on the first page, and the input and output connections end up deep in the stack of schematics. I'm not sure which is really better.
When should I consider putting multiple tracks into a buss?
I rarely do this, but its a matter of style (and convention in your workgroup).
How should I name busses, netlists, and the references to other pages?
I tend toward all-caps net names, but otherwise I don't have fixed rules. More disciplined organizations might have more detailed rules.
How should I place components to minimize the number of nets?
I prefer to place components to make the signal flow clear. I don't worry about the number of named nets.
What kind of comments should I include on a schematic?
Anything important for the layout guy to know (matched length traces, place bypass caps near ICs, etc.) Anything a future engineer might need to know if they're looking to replace an obsolete part. Non-obvious critical specs like higher-than-normal resistor power requirements or tight tolerances. Anything that has to be tuned in production (Like "tune pot to achieve 50% duty cycle" or whatever).
Where should I place the designation and value for horizontal and vertical components? Does it matter as long as I stay consistent?
I use vertical text for vertical components to allow more parts to fit cleanly on a sheet. Others (apparently) consider this a grave sin. Be consistent and be consistent with others in your organization.
Should I note component packaging & rating on the schematic? Meaning discrete vs SMD or if a specific resistor is high powered?
Specifying the package type for each part visibly on the schematic would be clutter. But obviously that information has to be in the design to get transferred to layout. As mentioned above mention nonobvious specs that might trip someone up if they have to replace an obsolete part or find an alternate vendor due to a shortage.
Your BOM (Bill of Materials) will need to specify an exact manufacturers part number (or a list of acceptable alternates called an AVL "approved vendor list") for each part.
Should I customize nets in different colors or widths?
I don't recommend this. I'd prefer to get schematics that make sense if printed out in black & white.
How should I version control schematics?
I store datecoded backups (like "mydesign_20120205.zip" on my own pc and a remote share drive. Definitely store a backup whenever you release a design (either to layout or to manufacturing).
Edit: There are better ways to do this (see comments) but a simple process like dated zip files is also perfectly workable.
What workflow should a single person use to keep designs organized?
Keep backups. Use all the tools you have available. If you aren't doing your own layout, keep good communication with the layout guy.
Best Answer
I personally go the old-fashioned route: I have a design notebook where I write down absolutely everything about the design decisions I make. Especially component and value choices, current calculations, power supply calculations, everything. I also document software/firmware decisions and notes on timing and resource usage.
Each notebook has a contents page to reference a specific part of the design (power supply, etc) and all the pages are numbered.
I have considered going digital a number of times but it is nice to have my notebook out in front of me while I work and I find writing formulae digitally to be quite awkward. It's much easier to write calculations out by hand.
When preparing a spec or formal documentation for a board design, I usually refer back to my notebook as a refresher of what I did (or I write the digital documentation at the same time). Even though this may seem like I'm doing the same thing twice, I find that my notebooks are pretty much all calculation and explanation for myself, where documentation is much less verbose and much more formal and explanatory for others. As such, I don't often find I'm writing the same thing twice.