Interesting thread. It sounds like people here haven't discovered tagging software. There is never a need to rerip a disc as Kublakhan seems to be suggesting. I would suggest Tag & Rename, it supports id3, ape, flac and multiple other tagging formats. I believe it costs a few bucks, but you will likely find that you use this program frequently. It has a gentle learning curve and is frankly invaluable when it comes to maintaining a digital library.
Kublakhan is correct when he states that it really doesn't matter which playback software you use in terms of sound (asuming asio or directsound v2.5 or something similar is being used). However, not all players are created equal when it comes to leaving your tags alone. Windows Media Player and the newest version of foobar are currently the worst offenders in this category usurping itunes old spot (although itunes now has plenty of options to turn tag screwing options off). However, it's all really a matter of preference--feel free to use whatever floats your boat. Just make sure to write protect your audio files before chucking them into some player's library.
As far as ripping is concerned, EAC is your only option if you care about audio at all.
As far as a library for managing and browsing your collection is concerned. 1000 cd's isn't large enough to pose a problem for any library that I'm aware of. Eventually, as your collection grows, you'll want to find a library that doesn't search via tag (as most do) but rather cache's the database to a text file and then searches that instead. It is much much faster, but at this stage of the game, largely irrelavant. I'm currently at just over 6,000 albums in FLAC--I ended up having to write a separate program to meet my browsing needs.