Yeah, I guess it depends what your appendix is. If it's sort of a companion piece, like a wiki or something, then hold it back and stick it online when your books sells a million copies. (Ex: Pottermore, Brightweavings.)
If it's part of the text--basically it's meta-fictional--then I'd put it in because it contributes to the story. (Ex: Tolkien.) The trick here is to know what you have. Don't throw in a big Tolkiensian appendix just because Tolkien did it. Tolkien's appendix is there because it works really closely with the story and the way he's telling it; there's this whole archival motif running throughout and his appendices and prologues are very much part of that.
I've been doing a pile of agent research lately and one thing I have seen fairly often are appeals to submit the whole book when the whole book is asked for. I think this more commonly comes up with prologues, but an appendix, if it's part of the meta-text, is in that same vein. If a reader's gonna read it, the agent probably wants to see it. The question to ask is whether a reader wants to read it. That's the question agents are going to ask, too.