If you just open Premiere projects in AE, use copy&paste of clips from PPro to AE and onlyimport footage from AE back into PPro, then that won't affect the general workflow. however, be aware that
a) the pixel aspect ratios have been corrected in CS4
b) MediaCore was updated in CS4
Therefore files captured with PPro CS3 may come over with incorrect PAR, cause warnings, if they are MediaCore formats (HDV,DV, certain QT formats, otehr MPEG stuff), or not come over at all. So the general gist of it is, that ideally you would upgrade both apps. Unfortunately I cannot even give you peace of mind by recommending the trial - for reasons of licensing cost the MPEG stuff is disabled there and you would not be able to verify that part. The rest works, though, so if that limitation is not relevant for you, it's still worth a spin...
The special integration features, like sending an After Effects Comp to Premiere Pro through Dynamic Link, will require not only that the versions are in sync but also that the applications are bought as part of Production Premium or Master Collection. Dynamic Link is a component that doesn't come with the point products, but as part of the larger suites.
In this regard, you may want to investigate if instead of upgrading AE CS3 to CS4 (or any individual app from CS3 to CS4), it could be convenient to use the option to upgrade from AE CS3 to Production Premium CS4. You would get the latest versions of AE, PPro, Encore, Photoshop, Illustrator and Flash, PLUS Dynamic Link support (in CS4, Dynamic Link doesn't work just from AE to PPro or Encore, but also also from PPro to AE and Encore).
Other features, like After Effects' ability to open a Premiere Pro sequence and translate it into an After Effects Composition, will work just fine with PPro CS3 projects. This is not related to Dynamic Link.
If you're fine rendering movies from PPro to AE or viceversa, this will also work well of course.
Thanks for the advice, but I'm not 100% sure I get you -- I work mostly with
footage captured from HDV, so does that mean I'm out of luck?
We would have to define "luck" first
If you want to render a video file from Premiere Pro CS3 and open it in AE CS4 or viceversa, it will work perfectly.
If you want to open in AE CS4 a project that you saved from PPro CS3 (so that every clip in the PPro timeline becomes a layer in the resulting AE Comp, and a lot of effects and settings are preserved), it should work fine. But, as Mylenium said, you may see a warning that asks your permission to update the pixel aspect. After that, it should be OK. The number of Premiere Pro effects and settings that are translated when you import a PPro project into AE grows with each release, so if you had PPro CS4 and AE CS4, it would be a bit better in that regard.
If you want to make use of Dynamic Link, so for example you simply drag an After Effects composition to Premiere Pro (or viceversa), and see it automatically updated in PPro if you make changes in the AE comp, then you need the versions to be in sync, and you also need them to be a part of Production Premium or Master Collection. Dynamic Link is not included with the apps when bought as individual products.