This dissertation investigates the syntax and morphology of several functional morphemes that display surface optionality in Indonesian. Three case studies consider how syntactic environments constrain optional realization. Chapter 2 investigates the declarative complementizers bahwa and kalau, which are disallowed in case of A-bar movement; I show that bahwa is also disallowed in wh-in situ questions that do not involve movement. These facts are developed into an analysis of wh phrases and the structure of wh questions in Indonesian. I also propose that the morpheme yang, as well as the null form of the complementizer, constitute a pattern of morphological wh-agreement on C. Chapter 3 discusses the verbal prefixes meN- and ber-, which have received varied analyses in the literature. I argue that meN- and ber- participate in wh-agreement resulting from A-bar movement, and argue against previous analyses that assume that A-movement results in a similar deletion. In addition, I differentiate between deterministic properties that are relevant in the syntax, and non-deterministic properties of meN- and ber- that are extra-syntactic. This distinction accounts for a number of puzzling properties that have been observed for these prefixes. Chapter 4 discusses possessor sub-extraction in Indonesian, with additional data from similar constructions in Javanese and Madurese. I pursue a novel analysis of the nominal suffix -nya, which is optional is possessive DPs: in possessor extraction, this suffix is a pronunciation of the head D. The analysis of wh-agreement is extended to the DP domain, where -nya marks A-bar movement on phase heads; the consequence is that DP is a phase for syntactic movement. One language-specific finding in this dissertation is that morphological wh-agreement applies across three domains: complementizers, verbs and possessive nominals. This has cross-linguistic implications for the phasehood of DP and wh-agreement patterns. More broadly, the dissertation contributes a syntactic approach to the analysis of variable morphemes, revealing how multiple factors constrain surface optionality.