Modifying your CSS for browser-specific support is never wrong - as long as you can easily contain it. As you'll notice, standards-compliant browsers, * cough * everything except MSIE, will never break with future releases. New W3C standards also don't break previous standards, they usually deprecate or extend previous standards at the most.
People have mentioned conditional comments which are great for handling IE. But you'll need a bit more for handling all browsers (mobile, gecko, webkit, opera, etc.). Usually you'll parse the incoming request headers to fetch the browser type and version from the User-Agent param. Based on that you can begin loading your CSS files.
I belive the way most of us do it is by:
- First developing for one standards-compliant browser (let's take FF for example)
- Once the CSS is complete you approach providig support for IE (this can be easily done with the conditional comments, as perviously mentioned)
- First create a CSS file that will fine tune everything for IE6 and any other version below
- Then create a CSS file that will handle everything for IE7
- Lastly, create a CSS file that will handle everything for IE versions of IE8 and greater
- Once IE9 comes out, make sure you set IE8+ handling to IE8 specific, and create a IE9+ CSS file with required fixes
- Finally, create an additional CSS file for webkit fixes
- If required, you can also create additional files to specifically target Chrome or Safari if required
Concerning browser specific CSS implementations, I usually group all of those in my main css file (you can easily do a search for those and replace them in one document if needed). So if something has to be transparent, I'd set both opacity and filters (MSIE) in the same block. Browsers just ignore implementations they don't support, so your safe. Specific implementations I'd tend to avoid are custom implementations (hey, I like the -moz box above the W3C one, but I just don't want to rely on it).
As it goes with CSS inheritance and overriding, you don't have to redefine all the CSS declarations and definitions in every CSS file. Each consecutively loaded CSS file should only contain the selector and specific definitions required for the fix, and nothing else.
What you end up with in the end is your (huge) main css file and others, containing a few lines each, for specific browser fixes - which sums up to something that's not that very hard to maintain and keep track of. It's a personal preference what browser your base css file will be based off, but usually you'll be targeting a browser that will create the least amount of issues for other browsers (so yes, developing for IE6 would be a very poor decision at that point).
As always, following good practices and being pragmatic and meticulous with selectors and specifics about each class and using frameworks will lead you down the path of goodness with seldom fixes required. Structuring your CSS files is a huge plus unless you want to end up with an unordered meaningless mess.