Eclipse 'Helios' (3.6), which was released this month, includes the new version of PDT (PHP development tools). I tried this out for Moodle development at work today. In my workspace I've got about six copies of Moodle (various OU and core versions) plus the plugins CVS, plus a few Java projects kicking around. So it's a fairly large PHP workspace.
Good news:
1) The new DLTK indexing means that referencing PHP functions (i.e. ctrl-click to jump to definition) is lightning-quick.
2) There's a beta version of Git support as part of Helios - I wouldn't recommend using this until it hits 1.0 personally, and um I don't think it can do merge/pull yet which is a bit of a snag... but moving toward mainstream support is still great news.
Bad news:
1) It uses more RAM than 3.5; you definitely need to increase heap in eclipse.ini from Eclipse default (384MB) to at least 1GB. Note - on 32-bit windows, the max you can set for this is slightly over a gig even if you have 3+GB RAM, so use 64-bit if possible.
Sometimes I saw it peg the RAM at around the 1GB, dragging performance to a crawl; pretty sure this is a memory leak.
2) When editing PHP files I get frequent errors, mostly stack overflow somewhere in DLTK analysis.
3) Because the git stuff is beta, although it shouldn't affect these projects (they don't use git) I thought maybe it might, so I uninstalled that. Didn't make any difference.
Basically I am sure Eclipse Helios is a great release in general and for Java development but, not entirely surprisingly, the PDT folks (Zend I guess) have dropped the ball again; this will probably be better once they get it fixed, but right now it isn't ready for use. I've gone back to the previous version - it might not be able to to reliably find definitions of things, but at least it can usually keep up with my typing and doesn't show an error dialog every ten minutes.
Eclipse Helios SR1 (aka 3.6.1) is due on September 24th. If you're considering upgrading, that would seem like a good date to try.