Up until a few days ago I was laboriously merging in changes in Subclipse by hand: copying files across manually, trying to make sure I didn't miss anything. Then I discovered the merge tool: Now I can merge in complex changes that would have taken hours in just a few minutes.
The process is remarkably simple: Start by right click the root of the tree that you want the code to be merged into (in the file browser) and go to Team -> Merge. This gives you a somewhat unintuitive dialog: it took me a while to figure out that it was only asking for a source to merge from (even though one section does say To:). For most reasonable cases you want to use the same SVN path in the From: and the To: sections. In the From revision box you will want to put the revision which you last merged in, and in the To section select Head Revision.
Now you're ready to go: just hit Merge and SVN will work its magic (although it might take a while - be patient). Once it has finished it will display a log of its actions in the Console window, most of it will have worked fine - but there will probably be some conflicts, marked with a red C. All you have to do here is locate the relevant files in the file browser, right click on them and hit Team -> Edit Conflicts. This will open a new editor window with two panes, you're version on the left and the other version on the right.
In the Edit Conflicts window all conflicts will be highlighted, and all you have to do is resolve them by making suitable changes to the left-hand pane and saving (this is easy: they're rarely more than a few lines of code). Once things are sorted out, right click on the file in the file browser again and select Team -> Mark as Resolved. Once you've resolved all the conflicts you're done. Subclipse really is a wonderful piece of software.
One last tip: I find it useful to commit my branch just before merging changes: that way if something goes wrong I just have to hit Team -> Revert and everything is better again.
Note: For those of you who haven't tried Eclipse, Subclipse is an Eclipse plugin that adds SVN support - I use it in conjunction with Pydev.