the official under development page has the summaries of patch 4.0.1 and 4.0.3. mmo-champion is reporting that there will be extended maintenance this tuesday (october 12, 2010), which is often an indicator of a patch.
what will we see in patch 4.0.1 that is significant to companion enthusiasts? not a whole lot that i can tell. this patch is mainly implementing graphical and game mechanic changes. one thing that will be interesting is the updated spellbook and companion pet tab. since i'm currently not on the PTR, i can only report what the new tab will look like as seen on the beta.
with the revamped tab you'll find your pets in your spellbook rather than your character window. companions are still listed in alphabetical order and unfortunately, and to my dismay, there is still no search feature for the pet section of your spellbook. but unlike the previous pet tab, each companion listed will also have its name shown with its summoning icon. this should make it more convenient to find that specific pet you'd like to bring out.
another thing to keep in mind is that if you're using any vanity pet related mods, you'll probably want to update them. 4.0.1 will be bringing about many UI changes, so many addons may end up malfunctioning once the patch is released.
that's pretty much it for patch 4.0.1 for pet collectors. there may be some other additions that i'm unaware of, but we'll just have to wait for the official patch to find out. :P
patch 4.0.3, in my eyes, is the big doozie for pre-cataclysm content. in this patch (release date is unknown) there will be huge changes to the landscape of azeroth. this could mean a few of the world dropped companions may be relocated or disappear (either permanently or temporarily). warcraftpets.com has a short list of which pets MIGHT BE endangered.
i really cannot stress the "might be" and "possibly" enough, because we just don't know for sure which companions will be or will not be around in cataclysm. it won't be made clear until the actual expansion is released. who knows? if some of these companions do go missing in patch 4.0.3, developers could still sneak them back in between the patch and the expansion release.
there is still time to obtain these potentially endangered companions, so don't panic. to prepare, though, i would definitely move them up in priority on your "to collect" list. there are many unknowns with the coming patches, so all we can do is hope for the best and prepare for the worst.
note 1: there is no sign of the feat of strength achievement (it was mentioned a while ago) that requires you to have acquired all the "rare" companions, such as the whelps and other potentially missing pets, on the beta. i can only hope that this is hinting that developers do intend to release cataclysm with all current pets (although some will probably have to be moved or obtained in a different way).
note 2: for those of you eager to start on the pet-rewarded guild achievements (which is probably everyone haha) - i'm not entirely sure when guild achievements will launch, but i'm 90% sure we will not be able to earn them until the actual expansion release. however, they may give us previews in the coming patches so we can at least see them on live servers. if blizzard does give us the ok to work on them pre-cataclysm, i would expect patch 4.0.3 to have that content. but again, i don't think they'll be out any time soon.