For eBay searches what I like to do is get a search that shows what I want - for example searching the vintage computer category for "-amiga -atari -apple -c64 -commodore" and so on, to remove everything I know I am not interested in, so that hopefully what's left is what I want (also including those "old computer parts" type listings that you need to see for yourself.) Then I add "&_rss=1" onto the end of the URL to get the search results in the form of an RSS feed, and I subscribe to that in my RSS reader. Since I already check my other RSS feeds daily, this means every day I see whatever has been newly listed in the last day or so, which means I never miss anything. It also allows me to snap up those rare 'buy it now' listings where something is very cheaply priced, even though I may not have been specifically looking for that part.
I also add RSS feeds to my reader for certain keywords and price ranges without specifying a category, so I can pick up things that are listed outside the normal categories - for example the ATX motherboards that can sell quite cheaply because they're listed in the industrial electronics category. Adding the price restriction (e.g. max $40) automatically screens out items I consider overpriced so I don't waste time sorting through them.
As for finding a good motherboard, familiarise yourself with the typical ATX layout. Most of the nonstandard motherboards you want to avoid have the I/O ports in funny places instead of the usual ATX cluster (typically only one row high and spread right across the back of the board), and often they have a riser card to stop the case being so tall, which means they have one big slot instead of multiple PCI, ISA and AGP slots.
Getting Dell stuff isn't as bad as it used to be. You can now buy adapters to allow normal ATX power supplies to plug in to those Dell motherboards that had a non-standard ATX connector, and I've seen converter cables that provide standard AC97 front panel connectors from the custom one on the Dell Sound Blaster Live. The only real issue is making sure you get one that's ATX and not one of their proprietary form factors, unless it comes in the case as well. One good thing about Dell is that all their chipset drivers are still online. I think Intel's are as well, but some other manufacturers are starting to remove the drivers for their older boards.
As others have said, the best bet is to find out the brand. If it's a brand that sold motherboards back in the day (Abit, Asus, Intel, Gigabyte, etc, etc.) then you'll probably be fine. Intel boards can be hard to identify as they typically aren't branded, but if you can find a model number that starts with AA then it's probably Intel. If there are grid references as well (A, B, C, etc. down one edge, and 1, 2, 3 across the other edge) then it's almost certainly Intel.
My personal preference is to go Intel where I can, because they were always the most reliable boards. Abit and Asus had a better reputation for overclocking, but to me overclocking a retro PC is a bit pointless because I could just get newer/faster parts instead. But since retro machines can be tricky to get going - they seem to get less reliable with age - I figure if you start with the most reliable parts to begin with, it will bring you less pain in the long run!
