I'm starting to learn Latin on my own and I have trouble with pronouncing words correctly very often. Does anyone know of a Latin dictionary with the IPA transcriptions of Latin words, preferably with classical or ecclesiastical pronunciation?
Wiktionary provides IPA transcriptions of Latin words. See for example their entry for malus (/ˈma.lus/ [ˈma.ɫʊs]).
But such a thing is generally less needed for Latin than for English, because Latin pronunciation is fully predictable from the spelling (as long as your dictionary has macra). This article has a good overview.
Computer tools for pronunciation annotation (IPA).
> espeak -v la --ipa -q vocabulum wɔkˈabʊlʊm
It works with many other languages too, and can be easily integrated into desktop dictionary lookup software (e.g. GoldenDict).
Classical Language Toolkit
Reconstruction of short and long vowels is a difficult task if they are not clearly distinguished in the printed text. In such situation, eSpeak produces incorrect transcriptions (Latinus > [lˈatɪnʊs]). An attempt to solve this problem was made in the Classical Language Toolkit's module Macronizer, however it often fails too. CLTK is a programming library, not a ready to use software.
As Draconis indicates, pronunciation of individual Latin words can be deduced if you know how to spell the words (including vowel lengths) and you know which kind of Latin you want. The pronunciation evolved over the classical period, and especially ecclesiastic pronunciation took many different forms in different eras and places. There are rare exceptions (see e.g. this and this), but you can quite safely ignore them at first.
What you need is a good Latin dictionary — some are available online — and a pronunciation guide for the relevant variant of Latin. I'm not sure what is the best source for pronunciation help like this, but the Wikipedia page for Latin pronunciation should be a good start.
If anyone wants to ask for pronunciation guides for different variants of Latin, please suggest the question in this meta post, as it would probably make a broad resource request.
Another computer tool is Collatinus. It has GUI, gives definition of the words, IPA pronunciation (classic), syllables, and marks stress.