Ars Technica runs a guide every few months with their recommended components to build a desktop PC at a few different price/power levels. Here's their most recent one, from last December:
Their advice is generally really good, so even if you don't end up buying the exact components they recommend, it's useful for establishing a baseline of what a good custom PC at a given point in time for a given amount of money looks like.
As to compatibility issues, if you mean "compatibility with Linux," those sorts of problems are much less common today than they used to be, at least for desktop PCs. Laptops still require some picky shopping if you're planning to run Linux on them (thanks to things like proprietary drivers for wireless radios, grumble grumble), but compatibility with desktop parts is pretty robust.
http://arstechnica.com/gadgets/guides/2011/12/ars-technica-s...
Their advice is generally really good, so even if you don't end up buying the exact components they recommend, it's useful for establishing a baseline of what a good custom PC at a given point in time for a given amount of money looks like.
As to compatibility issues, if you mean "compatibility with Linux," those sorts of problems are much less common today than they used to be, at least for desktop PCs. Laptops still require some picky shopping if you're planning to run Linux on them (thanks to things like proprietary drivers for wireless radios, grumble grumble), but compatibility with desktop parts is pretty robust.